WO2018226964A2 - Promoters from corynebacterium glutamicum and uses thereof in regulating ancillary gene expression - Google Patents

Promoters from corynebacterium glutamicum and uses thereof in regulating ancillary gene expression Download PDF

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WO2018226964A2
WO2018226964A2 PCT/US2018/036472 US2018036472W WO2018226964A2 WO 2018226964 A2 WO2018226964 A2 WO 2018226964A2 US 2018036472 W US2018036472 W US 2018036472W WO 2018226964 A2 WO2018226964 A2 WO 2018226964A2
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pcg0007
promoter
target gene
genes
heterologous
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PCT/US2018/036472
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English (en)
French (fr)
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WO2018226964A3 (en
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Zach Serber
Katherine G. GORA
Shawn P. MANCHESTER
Peter ENYEART
Alexander SHEARER
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Zymergen Inc.
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Priority to KR1020207000506A priority Critical patent/KR20200026881A/ko
Priority to US16/620,188 priority patent/US20200239897A1/en
Priority to CN201880045247.1A priority patent/CN110869504A/zh
Priority to CA3064777A priority patent/CA3064777A1/en
Priority to EP18740369.6A priority patent/EP3635117A2/en
Priority to JP2019567365A priority patent/JP2020524492A/ja
Publication of WO2018226964A2 publication Critical patent/WO2018226964A2/en
Publication of WO2018226964A3 publication Critical patent/WO2018226964A3/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/74—Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora
    • C12N15/77—Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora for Corynebacterium; for Brevibacterium
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P13/00—Preparation of nitrogen-containing organic compounds
    • C12P13/04—Alpha- or beta- amino acids
    • C12P13/08—Lysine; Diaminopimelic acid; Threonine; Valine
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/351—Conjugate
    • C12N2310/3519—Fusion with another nucleic acid
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2330/00—Production
    • C12N2330/50—Biochemical production, i.e. in a transformed host cell
    • C12N2330/51—Specially adapted vectors
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2830/00—Vector systems having a special element relevant for transcription
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2830/00—Vector systems having a special element relevant for transcription
    • C12N2830/55—Vector systems having a special element relevant for transcription from bacteria

Definitions

  • the disclosure relates to native promoters comprising polynucleotides isolated from
  • coryneform bacteria in particular Corynebacterium glutamicum
  • biomolecules such as amino acids, organic acids, vitamins, nucleosides and nucleotides.
  • Continuous efforts are being made to improve production processes. Said processes may be improved with respect to fermentation related measures such as, for example, stirring and oxygen supply, or the composition of nutrient media, such as, for example, sugar concentration during fermentation, nutrient feeding schedules, pH balance, metabolite removal, or the work-up into the product form, for example by means of ion exchange chromatography, or the intrinsic performance characteristics of the microorganism itself.
  • Performance characteristics can include, for example, yield, titer, productivity, by-product elimination, tolerance to process excursions, optimal growth temperature and growth rate.
  • One way to improve performance of a microbial strain is to increase the expression of genes that control the production of a metabolite. Increasing expression of a gene can increase the activity of an enzyme that is encoded by that gene. Increasing enzyme activity can increase the rate of synthesis of the metabolic products made by the pathway to which that enzyme belongs. In some instances, increasing the rate of production of a metabolite can unbalance other cellular processes and inhibit growth of a microbial culture. Sometimes, down regulating activity is important to improve performance of a strain. For example, re-directing flux away from by-products can improve yield. Accordingly, fine-tuning of expression levels of the various components simultaneously within a metabolic pathway is often necessary.
  • Promoters regulate the rate at which genes are transcribed and can influence transcription in a variety of ways. Constitutive promoters, for example, direct the transcription of their associated genes at a constant rate regardless of the internal or external cellular conditions, while regulatable promoters increase or decrease the rate at which a gene is transcribed depending on the internal and/or the external cellular conditions, e.g. growth rate, temperature, responses to specific environmental chemicals, and the like. Promoters can be isolated from their normal cellular contexts and engineered to regulate the expression of virtually any gene, enabling the effective modification of cellular growth, product yield and/or other phenotypes of interest.
  • a promoter is typically functionally linked to a heterologous target gene that is a component of the biosynthetic pathway that makes the target biomolecule in the host cell.
  • a component of the lysine biosynthetic pathway e.g., as defined in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway M00030
  • KEGG Kyoto Encyclopedia of Genes and Genomes
  • the present disclosure addresses these and other needs in the art.
  • the present disclosure is directed to a host cell containing a promoter polynucleotide sequence functionally linked to at least one heterologous ancillary target gene, wherein the ancillary target gene is not a component of the biosynthetic pathway for producing the target biomolecule.
  • the present disclosure provides methods for screening for, identifying, and using a promoter polynucleotide operably linked to a heterologous ancillary target gene to improve production of a target biomolecule.
  • the promoter polynucleotide comprises a sequence selected from: SEQ ID NO: l , SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, and SEQ ID NO: 8.
  • the promoter polynucleotide consists of a sequence selected from: SEQ ID NO: 1, SEQ ID NO:5, or SEQ ID NO:7.
  • the ancillary target gene is a gene that is classified under GOslim term GO:0003674; GO:0003677; GO:0008150; GO:0034641 ; or GO:0009058.
  • the ancillary target gene is a gene that is classified under, or under at least, 2, 3, 4, or 5 of the following GOslim terms GO:0003674; GO:0003677; GO:0008150; GO:0034641 ; or GO:0009058.
  • the ancillary target gene is selected from the genes of one or more, or all, of the following KEGG entries: M00010, M00002, M00007, M00580, or M00005.
  • the ancillary target gene is not a component of a biosynthesis pathway comprising genes of one or more, or all, of the following KEGG entries: M00016; M00525; M00526; M00527; M00030; M00433 M00031 ; M00020; M00018; M00021; M00338; M00609; M00017;
  • the disclosure provides a host cell containing at least a first and a second promoter polynucleotide sequence, wherein the first promoter is functionally linked to a first heterologous target gene, wherein the first heterologous target gene is a component of a biosynthetic pathway for producing a target biomolecule, and the second promoter is functionally linked to a second heterologous ancillary target gene that is not a component of the biosynthetic pathway for producing the target biomolecule.
  • the first promoter can be a native promoter comprising
  • both the first and the second promoter comprise a sequence selected from: SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, and SEQ ID NO: 8.
  • the promoter polynucleotide consists of a sequence selected from: SEQ ID NO: 1, SEQ ID NO:5, or SEQ ID NO:7.
  • One embodiment of the present disclosure relates to host cells comprising the first and/or second promoter polynucleotides described herein.
  • One embodiment of the present disclosure relates to recombinant vectors comprising the first promoter polynucleotide and/or second promoter polynucleotide described herein.
  • the first promoter polynucleotide is functionally linked to a first on-pathway target gene.
  • the second promoter polynucleotide is functionally linked to a first or second ancillary target gene.
  • One embodiment of the present disclosure relates to host cells comprising the combinations of promoter polynucleotides described herein.
  • One embodiment of the present disclosure relates to recombinant vectors comprising the combinations of promoter
  • each promoter polynucleotide is functionally linked to a different target gene.
  • the target genes are not part of the same metabolic pathway.
  • a first set of target genes are part of the same metabolic pathway and a second set of target genes are part of a different pathway.
  • One embodiment of the present disclosure relates to host cells transformed with the recombinant vectors described herein.
  • One embodiment of the present disclosure relates to host cells comprising at least one promoter polynucleotide functionally linked to an ancillary target gene; wherein the promoter polynucleotide comprises a sequence selected from: SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO: 3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8; wherein when the promoter polynucleotide comprises a sequence selected from: SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, or SEQ ID NO: 8, the target gene is other than the promoter polynucleotide's endogenous gene.
  • the host cell comprises at least two promoter polynucleotides, wherein each promoter polynucleotide is functionally linked to a different target gene.
  • One embodiment of the present disclosure relates to recombinant vectors comprising at least one promoter polynucleotide functionally linked to an ancillary target gene; wherein the promoter polynucleotide comprises a sequence selected from: SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO: 6, SEQ ID NO:7, and SEQ ID NO: 8; wherein when the promoter polynucleotide comprises a sequence selected from: SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, or SEQ ID NO: 8, the target gene is other than the promoter polynucleotide ' s endogenous gene .
  • the recombinant vector comprises at least two promoter polynucleotides, wherein each promoter polynucleotide is functionally linked to a different target gene.
  • the target genes are not part of the same metabolic pathway.
  • one target gene can be an on-pathway target gene for production of a target biomolecule, and the second target gene can be an ancillary target gene.
  • the transformed host cells comprise a combination of promoter polynucleotides functionally linked to a heterologous ancillary target gene or at least one heterologous ancillary target gene, wherein said combination of promoter polynucleotides comprises a promoter ladder.
  • the individual promoter polynucleotides can be in different transformed host cells and operably linked to the same heterologous ancillary target gene sequence.
  • said combination of promoter polynucleotides comprises at least one first promoter polynucleotide, and at least one second promoter polynucleotide.
  • the first promoter polynucleotide is selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 5, and SEQ ID NO: 7 and the second promoter polynucleotide is selected from the group consisting of: SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, and SEQ ID NO: 8 In some embodiments, said first and second promoter polynucleotide are in different host cells of a plurality of host cells and operably linked to the same heterologous ancillary target gene sequence.
  • the transformed host cells comprise a combination of promoter polynucleotides comprising a promoter ladder of two, three, four, five, six, seven, and/or eight different promoter polynucleotides.
  • said first, second, third, fourth, fifth, sixth, and/or seventh promoter polynucleotide are in different host cells of the plurality of transformed host cells and operably linked to the same heterologous ancillary target gene sequence.
  • the transformed host cells comprising the combination of promoter
  • each of the transformed host cells, substantially all of the transformed host cells, or a majority of the transformed host cells comprises a promoter polynucleotide operably linked to an on-pathway, a shell 1, and/or a shell 2 heterologous target gene.
  • One embodiment of the present disclosure relates to methods of modifying the expression of one or more ancillary target genes, comprising culturing a host cell described herein, wherein the modification of each ancillary target gene is independently selected from: up-regulating and down-regulating.
  • the ancillary target gene does not code for one or more polypeptides or proteins of a biosynthetic pathway of biomolecules such as an amino acid, organic acid, nucleic acid, protein, or polymer.
  • the ancillary target gene may code for one or more polypeptides or proteins of the biosynthetic pathway of a transcription factor, a signaling molecule, a component of the citric acid cycle, or a component of glycolysis.
  • Another embodiment of the present disclosure relates to methods of producing a biomolecule comprising culturing a host cell described herein, under conditions suitable for producing the
  • the ancillary target gene directly or indirectly enhances the biosynthesis of a biomolecule selected from: amino acids, organic acids, flavors and fragrances, biofuels, proteins and enzymes, polymers/monomers and other biomaterials, lipids, nucleic acids, small molecule therapeutics, protein or peptide therapeutics, fine chemicals, and nutraceuticals.
  • the biomolecule is an L-amino acid.
  • the L-amino acid is lysine.
  • the host cell belongs to the genus Corynebacterium. In some embodiments, the host cell belongs to the genus Corynebacterium. In some
  • the host cell is Corynebacterium glutamicum.
  • Fig. 1 presents a diagram of the genetic and biochemical pathway for the biosynthesis of the amino acid L-lysine. Genes that divert intermediates in the biosynthetic pathway (e.g. , pck, odx, icd, and horn) are underlined.
  • recombinant nucleic acid molecule refers to a recombinant DNA molecule or a recombinant RNA molecule.
  • a recombinant nucleic acid molecule is any nucleic acid molecule containing joined nucleic acid molecules from different original sources and not naturally attached together.
  • Recombinant RNA molecules include RNA molecules transcribed from recombinant DNA molecules.
  • a recombinant nucleic acid molecule includes a nucleic acid molecule comprising a promoter of SEQ ID NOs: 1 to 8 functionally linked to a heterologous target gene.
  • heterologous target gene refers to any gene or coding sequence that is not controlled in its natural state (e.g. , within a non -genetically modified cell) by the promoter to which it is operably linked in a particular genome.
  • all target genes functionally linked to non- naturally occurring promoters are considered “heterologous target genes”. More specifically, as promoter polynucleotide sequences of SEQ ID NOs: 1, 5, and 7 do not occur in nature, all functionally linked target gene sequences are "heterologous target gene” sequences. Similarly, all, e.g.
  • heterologous target genes can include one or more target genes that are part of an operon. That is, the endogenous promoter of an operon is replaced with a promoter polynucleotide sequence having a nucleic sequence of SEQ ID NOs: 1 to 8.
  • promoter polynucleotide sequence refers to nucleic acids having a sequence as recited in the associated SEQ ID NO.
  • a “metabolic pathway” or “biosynthetic pathway” is a series of substrate to product conversion reactions, each of which is catalysed by a gene product (e.g., an enzyme), wherein the product of one conversion reaction acts as the substrate for the next conversion reaction and which includes the conversion reactions from a feedstock to a target biomolecule.
  • the metabolic pathway is a pathway module as defined in the Kyoto Encyclopedia of Genes and Genomes KEGG database.
  • an "on-pathway" heterologous target gene is a heterologous target gene that encodes a gene product (e.g., an enzyme or a component of a multi -enzyme complex) that is in the metabolic pathway by which the target biomolecule is produced in the organism in which it is present.
  • the genes targeted for modification are those genes that are judged to be "on-pathway,” i.e., the genes for the metabolic enzymes known to be part of, or branching into or off of, the biosynthetic pathway for the molecule of interest (Keasling, JD. "Manufacturing molecules through metabolic engineering.” Science, 2010).
  • Methods such as flux balance analysis (“FBA”) (Segre et al, "Analysis of optimality in natural and perturbed metabolic networks.” PNAS, 2002) are known that can automate the discovery of such genes.
  • FBA flux balance analysis
  • a gene product e.g. , an enzyme or a component of a multi-enzyme complex
  • an ancillary or off-pathway heterologous target gene for production of the target biomolecule L-lysine is a gene that is not disclosed in KEGG pathway module M00016, M00030, M00031, M00433, M00525, M00526, or M00527, or preferably all thereof.
  • an ancillary or off-pathway heterologous target gene for production of the target biomolecule serine is a gene that is not disclosed in KEGG pathway module M00020.
  • an ancillary or off- pathway heterologous target gene for production of the target biomolecule threonine is a gene that is not disclosed in KEGG pathway module M00018.
  • an ancillary or off-pathway heterologous target gene for production of the target biomolecule cysteine is a gene that is not disclosed in KEGG pathway module M00021, M00338, or M00609, or preferably all thereof.
  • an ancillary or off-pathway heterologous target gene for production of the target biomolecule valine and/or isoleucine is a gene that is not disclosed in KEGG pathway module M00019.
  • an ancillary off-pathway heterologous target gene for production of the target biomolecule isoleucine is a gene that is not disclosed in KEGG pathway module M00535, or M00570, or preferably all thereof.
  • an ancillary or off-pathway heterologous target gene for production of the target biomolecule leucine is a gene that is not disclosed in KEGG pathway module M00432.
  • an ancillary or off-pathway heterologous target gene for production of the target biomolecule proline is a gene that is not disclosed in KEGG pathway module M00015.
  • an ancillary or off-pathway heterologous target gene for production of the target biomolecule ornithine is a gene that is not disclosed in KEGG pathway module M00028, M00763, or preferably all thereof.
  • an ancillary or off-pathway heterologous target gene for production of the target biomolecule histidine is a gene that is not disclosed in KEGG pathway module M00026.
  • aromatic amino acids such as tryptophan, tyrosine, and phenylalanine are produced via the shikimate pathway.
  • an ancillary or off-pathway heterologous target gene for production of the target biomolecule shikimate or an amino acid that is a biosynthetic product of the shikimate pathway e.g., one or more of the target biomolecules tryptophan, tyrosine, or phenylalanine
  • an ancillary or off-pathway heterologous target gene for production of the target biomolecule tryptophan is a gene that is not disclosed in KEGG pathway module M00022.
  • an ancillary or off-pathway heterologous target gene for production of the target biomolecule phenylalanine is a gene that is not disclosed in KEGG pathway module M00024.
  • an ancillary or off-pathway heterologous target gene for production of the target biomolecule tyrosine is a gene that is not disclosed in KEGG pathway module M00025, M00040, or the combination thereof.
  • a heterologous target gene that is a component of the biosynthetic pathway that produces L- lysine is one of the following genes, or an endogenous functional ortholog thereof in the organism in which it is present, asd, ask, aspB, cg0931, dapA, dapB, dapD, dapE, dapF, ddh, fbp, hom, icd, lysA, lysE, odx, pck, pgi, ppc, ptsG, pyc, tkt, or zwf
  • an ancillary or off-pathway heterologous target gene is a gene that is not one of the following genes, or an endogenous functional ortholog thereof in the organism in which it is present, asd, ask, aspB, cg
  • target genes are divided into priority levels, called “shells” and promoter polynucleotides are operably linked to one or more heterologous target genes of a shell, wherein the shell is comprised genes that are indirectly involved in target molecule production.
  • shell 1 genes are genes that encode biosynthetic enzymes directly involved in a selected metabolic pathway.
  • Shell 2 genes include genes encoding for non-shell 1 enzymes or other proteins within the biosynthetic pathway responsible for product diversion or feedback signaling.
  • “Shell 3” genes include regulatory genes responsible for modulating expression of the biosynthetic pathway or for regulating carbon flux within the host cell.
  • Shell 4" genes are the genes of a target organism that are not assigned to any one of shells 1-3. Example 5 describes allocation of genes in C. glutamicum into shells for systematic genome- wide perturbation of lysine production.
  • an ancillary heterologous target gene is a "shell 2," “shell 3,” and/or "shell 4" heterologous target gene for production of a target molecule.
  • an ancillary heterologous target gene is a "shell 3" and/or "shell 4" heterologous target gene for production of a target molecule.
  • the ancillary heterologous target gene is a "shell 3" heterologous target gene for production of a target molecule.
  • the ancillary heterologous target gene is a "shell 4" heterologous target gene for production of a target molecule.
  • the ancillary heterologous target gene is a "shell 2" heterologous target gene for production of a target molecule.
  • Exemplary target genes and their shell designation in the context of lysine production in C are illustrated.
  • Native C. glutamicum promoters were identified that satisfy both of the following criteria: 1) represent a ladder of constitutive promoters, i.e. , a plurality of promoters with incrementally increasing levels of promoter activity; and 2) encoded by short DNA sequences, ideally less than 100 base pairs.
  • a published data set describing global gene expression levels in C. glutamicum ATCC 13032 (Lee et al , Biotechnol Lett (2013) 35:709-717) was examined to identify genes that were constitutively expressed across different growth conditions. Genes whose expression level remained constant (defined as a ratio of expression between 0.33 and 3) across two growth conditions, namely chemostat growth in minimal media with and without the addition of hydrogen peroxide satisfied the first criterion.
  • the wild-type promoters Pcgl860, and Pcg3121 are not described in the literature.
  • the wild-type promoter Pcg0007-gyr5 is also not described in the literature, however, Neumann and Quinones, (J Basic Microbiol. 1997;37(l):53-69) describes regulation of gyrB gene expression in E. coli.
  • the wild-type promoter Pcg0755 is a known part of the methionine biosynthesis pathway (Suda et al, Appl Microbiol Biotechnol (2008) 81 :505-513; and Rey et al , Journal of Biotechnology 103 (2003) 51-65).
  • the wild- type promoter Pcg3381 is a tat A homolog.
  • the tatA pathway in Corynebacterium is described by Kikuchi et al , Applied and Environmental Microbiology, Nov. 2006, p. 7183-7192.
  • the strong constitutive promoter Pcg0007 was chosen for mutagenesis.
  • Four out of six positions in the predicted -10 element (TAAGAT) of Pcg0007 were randomized to generate both stronger and attenuated promoter variants (SEQ ID NOs 1, 5, and 7).
  • promoters comprising SEQ ID NOs: 1-8
  • the present inventors determined that one or more such promoters can be functionally linked to one or more heterologous target genes of a biosynthetic pathway to increase the production of a target biomolecule produced by that biosynthetic pathway in a host cell.
  • the identification and characterization of promoters of SEQ ID NOs: 1-8, and their use in upregaulting and/or downregulating expression of one or more on-pathway heterologous target genes to produce a target biomolecule are further described in PCT Appl. No.
  • the present inventors surprisingly discovered that functionally linking one or more such promoters to one or more ancillary or off-pathway heterologous target genes can be used to increase production of the target biomolecule or further increase production of the target biomolecule.
  • functionally linking one or more such promoters to one or more ancillary heterologous target genes can be used to increase production of the target biomolecule in a strain background that does not have a promoter functionally linked to a heterologous target gene that is a component of the biosynthetic pathway that produces the target biomolecule.
  • functionally linking one or more such promoters to one or more ancillary heterologous target genes can be used to increase production of the target biomolecule in a strain background that also comprises one or more promoters functionally linked to one or more heterologous target genes that are components of the biosynthetic pathway that produces the target biomolecule.
  • the one or more promoters functionally linked to one or more heterologous target genes that are components of the biosynthetic pathway for production of a target biomolecule can be selected from SEQ ID NOs: 1-8, SEQ ID NOs: 1, 5, and 7, and other promoters known in the art.
  • the one or more promoters functionally linked to one or more ancillary heterologous target genes that are not components of the biosynthetic pathway for production of a target biomolecule can be selected from SEQ ID NOs: 1-8, SEQ ID NOs: 1, 5, and 7, and other promoters known in the art.
  • one embodiment of the present disclosure relates to native promoters comprising polynucleotides isolated from C. glutamicum, and mutant promoters derived therefrom that together represent a ladder of constitutive promoters with incrementally increasing levels of promoter activity, wherein one or more of the ladder of promoters is functionally linked to a heterologous ancillary target gene for production of a target biomolecule.
  • a C. glutamicum promoter can be encoded by a short DNA sequence.
  • a C. glutamicum promoter can be encoded by a DNA sequence of less than 100 base pairs.
  • the promoters can be used in any strain background, including strains that also include a promoter functionally linked to a heterologous target gene that is in a biosynthetic pathway for production of a target biomolecule.
  • One embodiment of the present disclosure relates to a promoter polynucleotide comprising a sequence selected from: SEQ ID NO: 1 (Pcg0007_lib_39), SEQ ID NO:2 (Pcg l 860), SEQ ID NO:3 (Pcg0007), SEQ ID NO:4 (Pcg0755), SEQ ID NO:5 (Pcg0007_lib_265), SEQ ID NO:6 (Pcg3381), SEQ ID NO:7 (Pcg0007_lib_l 19), or SEQ ID NO: 8 (Pcg3121).
  • the present specification provides for, and includes, a promoter polynucleotide comprising of SEQ ID NO: 1 functionally linked to at least one heterologous ancillary target gene.
  • the present specification provides for, and includes, a promoter polynucleotide of SEQ ID NO:2 functionally linked to at least one heterologous ancillary target gene.
  • the present specification provides for, and includes, a promoter polynucleotide of SEQ ID NO: 3 functionally linked to at least one heterologous ancillary target gene.
  • the present specification provides for, and includes, a promoter polynucleotide of SEQ ID NO: 4 functionally linked to at least one heterologous ancillary target gene.
  • the present specification provides for, and includes, a promoter polynucleotide of SEQ ID NO: 5 functionally linked to at least one heterologous ancillary target gene.
  • the present specification provides for, and includes, a promoter polynucleotide comprising of SEQ ID NO: 5 functionally linked to at least one heterologous ancillary target gene.
  • the present specification provides for, and includes, a promoter polynucleotide of SEQ ID NO: 7 functionally linked to at least one heterologous ancillary target gene. In another embodiment, the present specification provides for, and includes, a promoter polynucleotide of SEQ ID NO: 8 functionally linked to at least one heterologous ancillary target gene.
  • a “promoter cassette” refers to the polynucleotide sequences comprising a promoter polynucleotide of SEQ ID NOs: 1 to 8 functionally linked to at least one heterologous ancillary target gene.
  • a "promoter cassette” may further include one or more of a linker polynucleotide, a transcription terminator following the ancillary target gene, a ribosome binding site upstream of the start codon of the ancillary target gene, and combinations of each.
  • One embodiment of the present disclosure relates to a promoter polynucleotide consisting of a sequence selected from: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO: 8.
  • the present specification provides for, and includes a promoter polynucleotide sequence of SEQ ID NO: 1.
  • the present specification provides for, and includes a promoter polynucleotide sequence of SEQ ID NO:5.
  • the present specification provides for, and includes a promoter polynucleotide sequence of SEQ ID NO:7.
  • a promoter cassette may be described by reference to the promoter name followed by the name of the heterologous target gene that is functionally linked to it.
  • the promoter of SEQ ID NO: 2, entitled Peg 1860, functionally linked to the gene zwf encoding the off- pathway glucose-6-phosphate 1 -dehydrogenase gene is referenced as Pcgl 860-zwf.
  • Pcg0007_39-lysA is the 0007_39 promoter of SEQ ID NO: 1 functionally linked to target gene lysA encoding the polypeptide diaminopimelate decarboxylase.
  • polynucleotides described herein refers to two or more polynucleotides that may be present as separate isolated sequences, as components of separate polynucleotide molecules, or as components of the same polynucleotide molecule, and combinations thereof.
  • polynucleotide molecules include chromosomes and plasmids.
  • the disclosure also relates to an isolated promoter polynucleotide, which essentially consists of a polynucleotide having the nucleotide sequence depicted in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO: 8.
  • the present specification provides for, and includes an isolated promoter polynucleotide of SEQ ID NO: 1.
  • the present specification provides for, and includes an isolated promoter polynucleotide of SEQ ID NO: 5.
  • the present specification provides for, and includes an isolated promoter polynucleotide of SEQ ID NO: 7.
  • a polynucleotide of no more than 1,000, no more than 800, no more than 700, no more than 600, no more than 500 or no more than 400 nucleotides in length and a polynucleotide of no more than 15,000, no more than 10,000, no more than 7,500, no more than 5,000, no more than 2,500, no more than 1,000, no more than 800, no more than 700, no more than 600, no more than 500, or no more than 400 nucleotides in length have been added to the 5 ' end and 3 ' end, respectively, of the polynucleotides of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO: 8.
  • any useful combination of the features from the preceding two lists of polynucleotides added to the 5' end and 3 ' end, respectively, of the polynucleotides of SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO: 8, is in accordance with the invention here.
  • "Useful combination” means, for example, a combination of features which results in an efficient recombination being carried out.
  • the use of additions of the same length flanking a DNA region to be replaced facilitates the transfer of the region by homologous recombination in the experimental procedure.
  • flanking homologous regions are advantageous for efficient recombination between circular DNA molecules but cloning of the replacement vector is made more difficult with increasing length of the flanks (Wang et al. , Molecular Biotechnology, 432:43-53 (2006)).
  • the specification provides for, and includes, homologous regions flanking a promoter polynucleotide sequence of SEQ ID NOs: 1 to 8 functionally linked to at least one heterologous ancillary target gene (e.g., the "promoter cassette”) to direct homologous recombination and replacement of a target gene sequence.
  • the homologous regions are direct repeat regions.
  • the homologous regions comprises between 500 base pairs (bp) and 5000 bp each of the target gene sequence flanking the promoter cassette. In an embodiment, the homologous regions comprises at least 500 bp each of the target gene sequence flanking the promoter cassette. In an embodiment, the homologous regions comprises at least 1000 bp ( 1 Kb) each of the target gene sequence flanking the promoter cassette. In an embodiment, the homologous regions comprises at least 2 Kb each of the target gene sequence flanking the promoter cassette. In an embodiment, the homologous regions comprises at least 5 Kb each of the target gene sequence flanking the promoter cassette.
  • the disclosure furthermore relates to an isolated promoter polynucleotide, which consists of the nucleotide sequence depicted in SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, or SEQ ID NO: 8.
  • the isolated promoter polynucleotide consists of the polynucleotide sequence of SEQ ID NO: 1.
  • the isolate promoter polynucleotide consists of the polynucleotide sequence of SEQ ID NO: 5.
  • the isolate promoter polynucleotide consists of the polynucleotide sequence of SEQ ID NO:7.
  • Polynucleotides consisting of deoxyribonucleotide monomers containing the nucleobases or bases adenine (A), guanine (G), cytosine (C) and thymine (T) are referred to as deoxyribo-polynucleotides or deoxyribonucleic acid (DNA).
  • Polynucleotides consisting of ribonucleotide monomers containing the nucleobases or bases adenine (A), guanine (G), cytosine (C) and uracil (U) are referred to as
  • the monomers in said polynucleotides are covalently linked to one another by a 3',5 '-phosphodiester bond.
  • a “promoter polynucleotide” or a “promoter” or a “polynucleotide having promoter activity” means a polynucleotide, preferably deoxyribopolynucleotide, or a nucleic acid, preferably
  • promoter ladder refers to a plurality of promoters with incrementally increasing levels of promoter activity.
  • promoter activity refers to the ability of the promoter to initiate transcription of an polynucleotide sequence into mRNA. Methods of assessing promoter activity are well known to those of skill in the art and include, for example the methods described in Example 2 of PCT/US 16/65464.
  • constitutive promoter refers to a promoter that directs the transcription of its associated gene at a constant rate regardless of the internal or external cellular conditions.
  • the promoters of the promoter ladder exhibit a range of promoter strengths in response to a stimuli (e.g. , in response to induction with a chemical agent, heat, cold, stress, phosphate starvation, etc).
  • the promoters of the promoter ladder exhibit a range of constitutive promoter strengths.
  • the strand complementary to the strand in SEQ ID NO: l, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO: 8 of the sequence listing is likewise a subject of the invention.
  • kits comprise combinations of promoter polynucleotides comprising at least two first promoter polynucleotides described herein.
  • kits comprise combinations of promoter polynucleotides comprising at least one first promoter polynucleotide described herein, and at least one second promoter polynucleotide comprising a sequence selected from: SEQ ID NO:2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, and SEQ ID NO: 8.
  • the kits comprise combinations of promoter polynucleotides comprising at least one first promoter polynucleotide described herein, and at least one second promoter polynucleotide consisting of a sequence selected from: SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, and SEQ ID NO:8.
  • heterologous target genes are polynucleotides the expression of which are controlled by the promoters described herein.
  • the heterologous target genes may be coding polynucleotides which code for one or more polypeptide (s) or non-coding polynucleotides such as non-coding RNAs.
  • a polynucleotide coding for a protein/polypeptide essentially consists of a start codon selected from the group consisting of ATG, GTG and TTG, preferably ATG or GTG, particularly preferably ATG, a protein-encoding sequence and one or more stop codon(s) selected from the group consisting of TAA, TAG and TGA.
  • the heterologous target genes can be "on-pathway,” or “off-pathway,” or a combination thereof.
  • RNA polymerase proteins such as RNA polymerase, "sigma factors” and transcriptional regulatory proteins.
  • mRNA messenger RNA
  • “Functionally linked” means in this context the sequential arrangement of the promoter polynucleotide according to the disclosure with a further oligo- or polynucleotide, resulting in transcription of said further polynucleotide to produce a sense RNA transcript.
  • the further polynucleotide is a target gene which codes for a polypeptide/protein and consists of the coding region for a polypeptide, starting with a start codon, including the stop codon and, where appropriate, including a transcription termination sequence, "functionally linked” then means the sequential arrangement of the promoter polynucleotide according to the invention with the target gene, resulting in transcription of said target gene and translation of the synthesized RNA.
  • each gene may be preceded by a ribosome-binding site. Where appropriate, a termination sequence is located downstream of the last gene.
  • the target gene preferably codes for one or more polypeptides or proteins of the biosynthetic pathway of biomolecules, preferably selected from the group of proteinogenic amino acids, non- proteinogenic amino acids, vitamins, nucleosides, nucleotides and organic acids.
  • the target gene preferably consists of one or more of the one-pathway and/or off-pathway target genes listed in Table 1 of EP 1 108 790 A2 which is hereby incorporated by reference.
  • the present specification provides for, and includes, recombinant nucleic acid molecules comprising a promoter polynucleotide sequence selected from the group consisting of SEQ ID NOs: 1 to 8 functionally linked to any one of the heterologous target genes identifiable in the Kyoto Encyclopedia of Genes and Genomes (KEGG) as genes involved in metabolic and biosynthetic pathways.
  • KEGG Kyoto Encyclopedia of Genes and Genomes
  • the KEGG database is available on the internet at genome.jp/kegg.
  • the target biomolecule is an amino acid, a protein, or a carbohydrate polymer, and one or more of the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more ancillary target genes of the citric acid cycle.
  • the ancillary target genes are selected from the genes in KEGG pathway M00010.
  • the target biomolecule is an amino acid, a protein, or a carbohydrate polymer and one or more of the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more ancillary target genes of the glycolysis pathway.
  • the ancillary target genes are selected from the genes in KEGG pathway M00002.
  • the target biomolecule is an amino acid, a protein, or a carbohydrate polymer and one or more of the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more ancillary target genes of the pentose phosphate pathway.
  • the ancillary target genes are selected from the genes in KEGG pathway M00007, or M00580, or the combination thereof.
  • the target biomolecule is an amino acid, a protein, or a carbohydrate polymer and one or more of the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more ancillary target genes of the PRPP biosynthesis pathway.
  • the ancillary target genes are selected from the genes in KEGG pathway M00005.
  • the target biomolecule is a specific amino acid or a set of amino acids, and one or more of the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more ancillary target genes selected from a metabolic pathway for production of a different amino acid or set of amino acids.
  • the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the lysine biosynthesis pathway as represented in KEGG map number 00300.
  • the one or more on-pathway target genes are selected from the Lysine succinyl-DAP biosynthesis pathway, M00016.
  • the one or more on- pathway target genes are selected from the lysine acetyl -DAP biosynthesis pathway, M00525.
  • the one or more on-pathway target genes are selected from the lysine DAP dehydrogenase biosynthesis pathway, M00526.
  • the one or more on-pathway target genes are selected from the lysine DAP aminotransferase biosynthesis pathway, M00527. In an embodiment, the one or more on-pathway target genes are selected from the AAA pathway biosynthesis pathway, M00030. In an embodiment, the one or more on-pathway target genes are selected from the lysine biosynthesis pathway from 2-oxoglutarate, M00433 or the lysine biosynthesis pathway mediated by LysW, M00031.
  • the present disclosure provides for, and includes, the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the serine biosynthesis pathway comprising genes of entry M00020.
  • the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the threonine biosynthesis pathway comprising genes of KEGG entry M00018.
  • the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the cysteine biosynthesis pathway comprising genes of KEGG entry M00021.
  • the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the cysteine biosynthesis pathway comprising genes of KEGG entry M00338. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the cysteine biosynthesis pathway comprising genes of KEGG entry M00609. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the methionine biosynthesis pathway comprising genes of KEGG entry M00017.
  • the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the valine/isoleucine biosynthesis pathway comprising genes of KEGG entry M00019. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the isoleucine biosynthesis pathway comprising genes of KEGG entry M00535. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the isoleucine biosynthesis pathway comprising genes of KEGG entry M00570.
  • the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the leucine biosynthesis pathway comprising genes of KEGG entry M00432. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the proline biosynthesis pathway comprising genes of KEGG entry M00015. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on- pathway target genes of the ornithine biosynthesis pathway comprising genes of KEGG entry M00028.
  • the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the ornithine biosynthesis pathway comprising genes of KEGG entry M00763. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the histidine biosynthesis pathway comprising genes of KEGG entry M00026. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the shikimate biosynthesis pathway comprising genes of KEGG entry M00022.
  • the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the tryptophan biosynthesis pathway comprising genes of entry M00023. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on- pathway target genes of the phenylalanine biosynthesis pathway comprising genes of KEGG entry M00024. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the tyrosine biosynthesis pathway comprising genes of KEGG entry M00025. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes of the tyrosine biosynthesis pathway comprising genes of KEGG entry M00040.
  • one or more of the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes described herein and one or more promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more ancillary target genes described herein, e.g., in a host cell, a genome of a host cell, an expression cassette, and/or a polynucleotide vector.
  • one or more of the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more on-pathway target genes described herein and one or more other promoter polynucleotide sequences are functionally linked to one or more ancillary target genes described herein, e.g. , in a host cell, a genome of a host cell, an expression cassette, and/or a polynucleotide vector.
  • one or more of the promoter polynucleotide sequences of SEQ ID NOs: 1 to 8 are functionally linked to one or more ancillary target genes described herein and one or more other promoter polynucleotide sequences are functionally linked to one or more on-pathway target genes described herein, e.g. , in a host cell, a genome of a host cell, an expression cassette, and/or a polynucleotide vector.
  • the present disclosure provides for, and includes, the promoter polynucleotide sequences of SEQ
  • the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the serine biosynthesis pathway comprising genes of entry M00020.
  • the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the threonine biosynthesis pathway comprising genes of KEGG entry M00018.
  • the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the cysteine biosynthesis pathway comprising genes of KEGG entry M00021.
  • the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the cysteine biosynthesis pathway comprising genes of KEGG entry M00338. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the cysteine biosynthesis pathway comprising genes of KEGG entry M00609. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the methionine biosynthesis pathway comprising genes of KEGG entry M00017.
  • the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the valine/isoleucine biosynthesis pathway comprising genes of KEGG entry M00019. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the isoleucine biosynthesis pathway comprising genes of KEGG entry M00535. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the isoleucine biosynthesis pathway comprising genes of KEGG entry M00570.
  • the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the leucine biosynthesis pathway comprising genes of KEGG entry M00432. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the proline biosynthesis pathway comprising genes of KEGG entry M00015. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the ornithine biosynthesis pathway comprising genes of KEGG entry M00028.
  • the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the ornithine biosynthesis pathway comprising genes of KEGG entry M00763. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the histidine biosynthesis pathway comprising genes of KEGG entry M00026. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the shikimate biosynthesis pathway comprising genes of KEGG entry M00022.
  • the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the tryptophan biosynthesis pathway comprising genes of entry M00023. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the phenylalanine biosynthesis pathway comprising genes of KEGG entry M00024. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the tyrosine biosynthesis pathway comprising genes of KEGG entry M00025. In an embodiment, the promoter polynucleotide sequences of SEQ ID NOs: 1, 5 or 7 are functionally linked to one or more target genes of the tyrosine biosynthesis pathway comprising genes of KEGG entry M00040.
  • the present specification provides for, and includes, recombinant nucleic acid molecules comprising a promoter polynucleotide sequence selected from the group consisting of SEQ ID NOs: 1 to 8 functionally linked to any one of the heterologous on- or off-pathway target genes from Corynebacterium glutamicum ATCC 13032 provided in Table 2 or any Corynebacterium glutamicum equivalent thereof. Sequence start and end positions correspond to genomic nucleotide accession NC_003450.3. It will be understood by those of ordinary skill in the art that corresponding genes exist in other strains of C.
  • the present specification provides for, and includes a recombinant nucleic acid molecule comprising a promoter polynucleotide sequence of SEQ ID NO: 1 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes a recombinant nucleic acid molecule comprising a promoter polynucleotide sequence of SEQ ID NO:2 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes a recombinant nucleic acid molecule comprising a promoter polynucleotide sequence of SEQ ID NO: 3 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes a recombinant nucleic acid molecule comprising a promoter polynucleotide sequence of SEQ ID NO: 4 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes a recombinant nucleic acid molecule comprising a promoter polynucleotide sequence of SEQ ID NO: 5 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes a recombinant nucleic acid molecule comprising a promoter polynucleotide sequence of SEQ ID NO:6 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes a recombinant nucleic acid molecule comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes a recombinant nucleic acid molecule comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a heterologous target gene recited in Table 2.
  • Table 2 Target genes from Corynebacterium glutamicum according to the present specification
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 1 functionally linked to an on- or off- pathway heterologous target gene recited in Table 2.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:2 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes a recombinant vector comprising a promoter
  • polynucleotide sequence of SEQ ID NO: 3 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:4 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 5 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:6 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 1 functionally linked to an on- or off-pathway heterologous target gene recited in Table 2.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:2 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 3 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:4 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 5 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 6 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a heterologous target gene recited in Table 2.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 1 functionally linked to an on- or off-pathway heterologous target gene recited in Table 3.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:2 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 3 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:4 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 5 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 6 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 1 functionally linked to an on- or off- pathway heterologous target gene recited in Table 3.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:2 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 3 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:4 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 5 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:6 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a heterologous target gene recited in Table 3. In an embodiment, the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 1 functionally linked to an on or off-pathway heterologous target gene recited in Table 3.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 2 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 3 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 4 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 5 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 6 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a heterologous target gene recited in Table 3.
  • the present specification provides for a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence selected from the group consisting of SEQ ID NOs: 1 to 8 functionally linked to any one of the on- or off-pathway heterologous target genes from Corynebacterium glutamicum ATCC 13032 provided in Table 4 or their Corynebacterium glutamicum equivalent thereof. Sequence start and end positions correspond to genomic nucleotide accession NC_003450.3. It will be understood by those of ordinary skill in the art that corresponding genes exist in other strains of C. glutamicum and may be readily identified from Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 1 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:2 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 3 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:4 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 5 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 6 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 3 functionally linked to an on- or off- pathway heterologous target gene recited in Table 4. In an embodiment, the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:4 functionally linked to a heterologous target gene recited in Table 4. In an embodiment, the present specification provides for, and includes a recombinant vector comprising a promoter
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 6 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 1 functionally linked to an on- or off-pathway heterologous target gene recited in Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:2 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 3 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:4 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 5 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 6 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a heterologous target gene recited in Table 4.
  • the present specification provides for a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence selected from the group consisting of SEQ ID NOs: 1 to 8 functionally linked to any one of the off-pathway heterologous target genes from Corynebacterium glutamicum ATCC 13032 provided in Table 5 or their Corynebacterium glutamicum equivalent thereof. Sequence start and end positions correspond to genomic nucleotide accession NC_003450.3. It will be understood by those of ordinary skill in the art that corresponding genes exist in other strains of C.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 1 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:2 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 3 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:4 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 5 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 6 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 3 functionally linked to an off-pathway heterologous target gene recited in Table 5.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 4 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 5 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 6 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 1 functionally linked to an off-pathway heterologous target gene recited in Table 5.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 2 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 3 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 4 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 5 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 6 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a heterologous target gene recited in Table 5.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 1 functionally linked to an off-pathway heterologous target gene recited in Table 10. In an embodiment, the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:2 functionally linked to an off-pathway heterologous target gene recited in Table 10. In an embodiment, the present specification provides for, and includes a recombinant vector comprising a promoter
  • polynucleotide sequence of SEQ ID NO: 3 functionally linked to an off-pathway heterologous target gene recited in Table 10.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:4 functionally linked to a heterologous target gene recited in Table 10.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:5 functionally linked to a heterologous target gene recited in Table 10.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 6 functionally linked to a heterologous target gene recited in Table 10. In an embodiment, the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a heterologous target gene recited in Table 10. In an embodiment, the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a heterologous target gene recited in Table 10.
  • the present specification provides for a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence selected from a plurality of promoter polynucleotides comprising a promoter ladder.
  • the host cell is a component of a plurality of transformed host cells comprising the promoter ladder, e.g. , wherein each cell of the plurality comprises a different promoter polynucleotide of the promoter ladder.
  • the promoter polynucleotides of the promoter ladder, in the same or different transformed host cells of the plurality are operably linked to the same heterologous, e.g. , ancillary, target gene.
  • the heterologous target gene is a shell 2, a shell 3, and/or a shell 4 heterologous target gene. In some cases, the heterologous target gene is a shell 3, and/or a shell 4 heterologous target gene. In some cases the heterologous target gene is a shell 4 heterologous target gene. In some cases, the heterologous target gene is a shell 2 heterolgous target gene. In some cases, the heterologous target gene is a shell 3 heterologous target gene. In some cases, the heterologous target gene is a heterologous target gene from Corynebacterium glutamicum, such as the heterologous target genes provided in Table 10, or optionally any one of the tables described herein. Sequence start and end positions in Table 10 correspond to genomic nucleotide accession NC_003450.3. It will be understood by those of ordinary skill in the art that corresponding genes exist in other strains of C. glutamicum and may be readily identified from the present disclosure.
  • the promoter polynucleotides comprising the promoter ladder are selected from the group consisting of SEQ ID NOs: 1 to 8 functionally linked to an off-pathway heterologous target gene, e.g. , a shell 2, a shell 3, and/or a shell 4 heterologous target gene, an off-pathway heterologous target gene provided in Table 10, or optionally an off pathway target gene in any one of the tables described herein.
  • the heterologous target gene is a shell 4 heterologous target gene.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 1 functionally linked to a shell 2, a shell 3, and/or a shell 4 heterologous target gene, e.g. , a heterologous target gene recited in Table 10.
  • the heterologous target gene is a shell 4 heterologous target gene.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 2 functionally linked to a shell 2, a shell 3, and/or a shell 4 heterologous target gene, e.g.
  • the heterologous target gene is a shell 4 heterologous target gene.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 3 functionally linked to a shell 2, a shell 3, and/or a shell 4 heterologous target gene, e.g. , a heterologous target gene recited in Table 10.
  • the heterologous target gene is a shell 4 heterologous target gene.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 4 functionally linked to a shell 2, a shell 3, and/or a shell 4 heterologous target gene, e.g. , a heterologous target gene recited in Table 10.
  • the heterologous target gene is a shell 4 heterologous target gene.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 5 functionally linked to a shell 2, a shell 3, and/or a shell 4 heterologous target gene, e.g. , a heterologous target gene recited in Table 10.
  • the heterologous target gene is a shell 4 heterologous target gene.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 6 functionally linked to a shell 2, a shell 3, and/or a shell 4 heterologous target gene, e.g. , a heterologous target gene recited in Table 10.
  • the heterologous target gene is a shell 4 heterologous target gene.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a shell 2, a shell 3, and/or a shell 4 heterologous target gene, e.g. , a heterologous target gene recited in Table 10.
  • the heterologous target gene is a shell 2 heterologous target gene.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a functionally linked to a shell 2, a shell 3, and/or a shell 4 heterologous target gene, e.g. , a heterologous target gene recited in Table 10.
  • the heterologous target gene is a shell 4 heterologous target gene.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 3 functionally linked to an off-pathway heterologous target gene recited in Table 10. In an embodiment, the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO:4 functionally linked to a heterologous target gene recited in Table 10. In an embodiment, the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 5 functionally linked to a heterologous target gene recited in Table 10.
  • the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 6 functionally linked to a heterologous target gene recited in Table 10. In an embodiment, the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a heterologous target gene recited in Table 10. In an embodiment, the present specification provides for, and includes a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a heterologous target gene recited in Table 10.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 1 functionally linked to an off-pathway heterologous target gene recited in Table 10.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 2 functionally linked to a heterologous target gene recited in Table 10.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 3 functionally linked to a heterologous target gene recited in Table 10.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 4 functionally linked to a heterologous target gene recited in Table 10.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 5 functionally linked to a heterologous target gene recited in Table 10.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 6 functionally linked to a heterologous target gene recited in Table 10.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 7 functionally linked to a heterologous target gene recited in Table 10.
  • the present specification provides for, and includes, a host cell transformed with a recombinant vector comprising a promoter polynucleotide sequence of SEQ ID NO: 8 functionally linked to a heterologous target gene recited in Table 10.
  • a host cell refers to an organisms described below in the section entitled
  • a host cell may comprise one or more promoter cassettes as described herein.
  • the target gene is associated with a biosynthetic pathway producing a biomolecule selected from: amino acids, organic acids, flavors and fragrances, biofuels, proteins and enzymes, polymers/monomers and other biomaterials, lipids, nucleic acids, small molecule therapeutics, protein therapeutics, fine chemicals, and nutraceuticals.
  • the target gene is associated with a biosynthetic pathway producing a secondary metabolite selected from: antibiotics, alkaloids, terpenoids, and polyketides.
  • the target gene is associated with a metabolic pathway producing a primary metabolite selected from: alcohols, amino acids, nucleotides, antioxidants, organic acids, polyols, vitamins, and lipids/fatty acids.
  • the target gene is associated with a biosynthetic pathway producing a macromolecule selected from: proteins, nucleic acids, and polymers
  • L-amino acids may enhance, in particular to overexpress one or more enzymes of the respective biosynthesis pathway, glycolysis, anaplerosis, citric acid cycle, pentose phosphate cycle, amino acid export and optionally regulatory proteins.
  • genes selected from the following group may be enhanced, in particular overexpressed: the gene dapA coding for dihydrodipicolinate synthase (EP-B 0 197 335); the gene eno coding for enolase (DE:
  • L-amino acids also to attenuate, in particular to reduce, the expression of one or more genes selected from the group: the gene pck coding for phosphoenol pyruvate carboxykinase (DE 199 50 409.1; DSM 13047); the gene pgi coding for glucoses- phosphate isomerase (U.S. Pat. No. 6,586,214; DSM 12969); the gene poxB coding for pyruvate oxidase (DE: 1995 1975.7; DSM 13114); and the gene zwa2 coding for the Zwa2 protein (DE: 19959327.2, DSM 13113).
  • the gene pck coding for phosphoenol pyruvate carboxykinase DE 199 50 409.1; DSM 13047
  • the gene pgi coding for glucoses- phosphate isomerase U.S. Pat. No. 6,586,214; DSM 12969
  • amino acids in particular L-lysine
  • the promoter according to the disclosure can thus be used in each case for overexpressing or underexpressing the target gene in C. glutamicum.
  • the heterologous ancillary target genes are shell 2, shell 3, and/or shell 4 target genes. In some cases, the heterologous ancillary target genes are shell 3 and/or shell 4 target genes. In some cases, the heterologous ancillary target genes are shell 4 target genes.
  • the methods involve screening a library of transformed host cells, wherein individual transformed host cells of the library comprise a different
  • promoter polynucleotide operably linked heterologous ancillary target gene
  • Such combinations can then be identified from the library that improve target biomolecule production and used for manufacture of target biomolecule or further optimized.
  • the methods can include one or more steps of providing such a library, and/or screening such a library, and/or identifying transformants exhibiting improved target molecule production, and/or isolating such improved transformants, and/or storing or expanding such improved transformants.
  • the promoter polynucleotides comprise a promoter ladder.
  • transformed host cells of the library further comprise an on-pathway modification.
  • the on-pathway modification is the same for all, essentially all, substantially all, or a majority of the transformed cells of the library.
  • all, essentially all, substantially all, or a majority of the transformed cells of the library can comprise a promoter polynucleotide operably linked to the on-pathway heterologous target gene lysA and/or one or more other promoter polynucleotide(s) operably linked to on-pathway heterologous target gene(s).
  • the transformed host cells comprise a wild-type strain background such that endogenous on-pathway target genes are operably linked to their corresponding endogenous promoters.
  • the library of transformed cells can comprise a promoter ladder, wherein the individual promoter polynculeotides of the promoter ladder are in different cells of the library.
  • different promoter polynucleotides of the promoter ladder are operably linked to the same heterologous ancillary target gene in the different transformed cells.
  • the minium library size is eight cells, one cell containing each possible [promoter polynucleotide : operably linked heterologous ancillary target gene] combination, or nine cells where one cell is a control cell without a promoter polynucleotide of the promoter ladder.
  • the library of transformed host cells can contain a plurality (e.g., >10; >100; >1,000; 10-1,000; 10-10,000; or 100-100,000) of redundant copies of the minimal cellular set, of the library or a subset thereof.
  • the library can further comprise an additional set of cells for each interrogated heterologous ancillary target gene, such that each interrogated heterologous ancillary target gene is operably linked to each of the different promoter polynucleotides of the promoter ladder in a different cell.
  • This provides a set of cells, where each cell in the library is an experiment interrogating a different [promoter polynucleotide :
  • the library can be provided by a number of techniques available to one of skill in the art. For example, a plurality of host cells having a selected background (e.g. , modified for lysA overexpression) can be transformed with a library of recombinant vectors under conditions such that substantially all transformants are singly modified to contain a single [promoter polynucleotide operably linked heterologous ancillary target gene] combination.
  • the recombinant vectors can be integrating vectors, such that the providing comprises engineering the genome of the host cell.
  • the transformants can be isolated, stored, and/or expanded, and optionally assayed for target molecule production.
  • Exemplary isolating methods include without limitation limiting dilution, plating, streaking, and/or colony picking.
  • Exemplary storage methods include without limitation cryopreservation or sporulation.
  • transformants can be isolated, mixed with a suitable cryoprotectant (e.g. , glycerol), cryogenically frozen under conditions suitable to limit ice crystal formation, and stored.
  • a suitable cryoprotectant e.g. , glycerol
  • the interrogated heterologous ancillary target genes can be assayed in plurality of (e.g. , two or more) different on-pathway modification backgrounds.
  • the assay of different on-pathway backgrounds can be performed simultaneously, e.g. , in parallel, or sequentially.
  • the library of transformed host cells for increasing production of lysine can comprise a first sub-library of transformed host cells having a lysA overexpression modification and interrogating a plurality of
  • a library of transformed host cells for increasing production of lysine can comprise transformed host cells having a background comprising: an on-pathway lysA overexpression modification; an off-pathway pgi overexpression modification; and various
  • promoter polynucleotide operably linked heterologous ancillary target gene combinations.
  • the method includes identifying a host cell from the plurality of host cells that exhibits increased production of the target biomolecule.
  • the identifying step includes a reproducibility filter to identify host cells, and the underlying [promoter polynucleotide operably linked heterologous ancillary target gene] combinations that reproducibly exhibit increased production of the target biomolecule.
  • the identifying step can assay redundant copies of each [promoter polynucleotide operably linked heterologous ancillary target gene] combination and identify combinations that exhibit reproducibly improved target biomolecule production in all, substantially all, or a majority of the redundant copies.
  • a statistical filter can be applied to exclude combinations that do not meet a selected level of statistical significance (e.g. , p ⁇ 0.05, 0.01, 0.005, or 0.001).
  • the method can comprise an iterative method of providing a library.
  • a library can be provided, cultured, and one or more host cells exhibiting increased production of target biomolecule can comprise the background strain for a second round of library generation and screening.
  • a subsequent iteration creates a new host cell library comprising individual host cells harboring unique genetic variations that are a combination of genetic variation selected from amongst at least two individual host cells of a preceding host cell library. Iterations can be performed multiple times until a resulting host cell has acquired a selected level of target biomolecule production improvement; until further rounds of providing and screening a library exhibit diminishing improvement; or until improvement pleateus.
  • At least one round interrogates heterologous ancillary taget genes.
  • on-pathway genes can be interrogated in earlier or later rounds of library generation and screening, optionally in combination with further interrogation of heterologous ancillary target genes.
  • the target gene is positioned downstream of the promoter polynucleotide according to the invention, i.e. at the 3' end, such that both polynucleotides are functionally linked to one another either directly or by means of a linker oligonucleotide or linker polynucleotide. Preference is given to the promoter and the target gene being functionally linked to one another by means of a linker
  • linker oligonucleotide or linker polynucleotide consists of deoxyribonucleotides .
  • the expression “functionally linked to one another directly” means that the nucleotide at the 3' end of the promoter polynucleotide, e.g. , SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:
  • SEQ ID NO:3 SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO:8, is linked directly to the first nucleotide of the start codon of a target gene. This results in "leaderless" mRNAs which start immediately with the 5 '-terminal AUG start codon and therefore do not have any other translation initiation signals.
  • the expression "functionally linked to one another by means of a linker oligonucleotide” means that the nucleotide at the 3' end of the promoter polynucleotide, e.g., SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO:8, is linked by an oligonucleotide of 1, 2, 3, 4 or 5 nucleotides in length to the first nucleotide of the start codon of a target gene.
  • the expression "functionally linked to one another by means of a linker polynucleotide” means that the nucleotide at the 3 ' end of the promoter polynucleotide, e.g. , SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO: 8, is linked by a polynucleotide of from 6 to no more than 600 nucleotides in length to the first nucleotide of the start codon of a target gene.
  • the expression "functionally linked to one another” means that the target gene is bound to the promoter polynucleotide according to the invention in such a way that transcription of the target gene and translation of the synthesized RNA are ensured.
  • the linker polynucleotide is: 6 - 600, 6 - 500, 6 - 400, 6 - 300, 6 - 200, 6 - 180, 6 -160, 6 - 140, 6 - 120, 6 - 100, 6 - 80, 6 - 60, 6
  • the linker polynucleotide is 20, 21, 22, 23, 24, or 25 nucleotides in length because this produces preferably functional constructs.
  • the disclosure further relates accordingly to an isolated promoter polynucleotide, essentially consisting of a promoter polynucleotide, e.g. , SEQ ID NO: l, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:
  • SEQ ID NO:4 SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO: 8, which, via the nucleotide at its 3' end, is functionally linked, directly or by means of a linker polynucleotide which ensures translation of RNA, to a target gene which contains at its 5' end an ATG or GTG start codon and codes for one or more off-pathway polypeptide(s). Preference is given to the promoter and target gene being functionally linked to one another by means of a linker polynucleotide.
  • the disclosure furthermore also relates to an isolated polynucleotide, essentially consisting of a promoter polynucleotide, e.g. , SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO: 8, which, via the nucleotide at its 3' end, is functionally linked to a linker oligonucleotide.
  • a promoter polynucleotide e.g. , SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO: 8
  • the disclosure furthermore relates to an isolated polynucleotide, essentially consisting of a promoter polynucleotide, e.g. , SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO: 8, which, via the nucleotide at its 3' end, is functionally linked to a linker polynucleotide which ensures translation of RNA.
  • a promoter polynucleotide e.g. , SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO: 8
  • the term "essentially” means that a polynucleotide of no more than 1,000, no more than 800, no more than 700, no more than 600, no more than 500, or no more than 400 nucleotides in length has been added to the 5 ' end of the promoter polynucleotide, e.g.
  • flank at the 3 ' end of the linker oligo- or polynucleotide increases in length to no more than 15,000 nucleotides when the 3 ' end is functionally linked to a target gene which contains at its 5 ' end an ATG or GTG start codon and codes for one or more polypeptide(s).
  • linker polynucleotide ensure translation of RNA in an advantageous manner.
  • the linker polynucleotide which ensures translation of RNA, and the target gene coding for one or more polypeptide(s), which has an ATG or GTG start codon at its 5 ' end functional nucleotide sequences required for cloning may be incorporated into said polynucleotides at their 5 ' and 3' ends and are at least partially retained even after said cloning.
  • nucleotide sequence required for cloning here represents any REII (type II restriction endonuclease) cleavage site present, whose sequence normally consists of from 4 to 8 nucleotides.
  • site-specific mutagenesis by means of mutagenesis primers or a de novo gene synthesis e.g. by GENEART AG (Regensburg, Germany)
  • mutagenesis primers or a de novo gene synthesis e.g. by GENEART AG (Regensburg, Germany)
  • GENEART AG e.g. by GENEART AG (Regensburg, Germany)
  • a de novo gene synthesis e.g. by GENEART AG (Regensburg, Germany) of the nucleotide sequences to remove cleavage sites for restriction endonucleases may introduce silent mutations into the sequence in order to enable said cleavage sites to be used advantageously for subsequent cloning steps.
  • polynucleotide resulting from the promoter according to the invention being functionally linked to the linker polynucleotide which ensures translation of RNA is also referred to as expression unit herein below.
  • the disclosure furthermore relates to the use of the promoter according to the invention or of the expression unit according to the invention for expressing target genes or polynucleotides in
  • the promoter according to the invention or the expression unit according to the invention ensures transcription and translation of the synthesized RNA, preferably mRNA, into a polypeptide.
  • the term "host cell” refers to a transformed cell of a microorganism.
  • the present disclosure provides for, and includes, transformed host cells comprising the recombinant nucleic acids and recombinant vectors described in detail above.
  • the present disclosure further provides for, and includes, host cells transformed with two recombinant nucleic acids.
  • the host cells are transformed with three recombinant nucleic acids.
  • the nucleic acids may be selected from biosynthetic pathways based on the overall effect on the yield of the desired product. There is no practical limit the number of recombinant nucleic acids that may be incorporated into the host cells of the present specification. Expression is preferably carried out in microorganisms of the genus Corynebacterium. Preference is given to strains within the genus
  • Corynebacterium which are based on the following species: C. efficiens, with the deposited type strain being DSM44549; C. glutamicum, with the deposited type strain being ATCC13032; and C.
  • ammoniagenes with the deposited type strain being ATCC6871.
  • Very particular preference is given to the species C. glutamicum.
  • polynucleotides that code for polypeptides having a property, preferably enzyme activity, which are not present or detectable in the corresponding host are not present or detectable in the corresponding host.
  • Yukawa et al. describe expression of Escherichia coli genes for utilizing D- xylose in C. glutamicum R under the control of the constitutive Ptrc promoter (Applied Microbiology and Biotechnology 81, 691-699 (2008)).
  • the present specification provides for, and includes host cells such as C. glutamicum having two or more genes of a biosynthetic pathway under the control of the promoter polynucleotide sequences described above.
  • one or more target genes e.g. , ancillary target genes, and/or shell 2, and/or shell 3, and/or 4 target genes
  • one or more target genes are placed under the control of a promoter polynucleotide sequence having as sequence of SEQ ID NOs: 1, 5 or 7 as described above.
  • C. glutamicum host cells have two target genes under the control of the promoters having sequences of SEQ ID NOs: 1 to 8. In certain other embodiments according to the present specification, C. glutamicum host cells have two target genes under the control of the promoters having sequences of SEQ ID NOs: 1, 5 or 7. Using homologous
  • the promoters of the present disclosure replace the endogenous promoter and endogenous sequence to prepare a promoter functionally linked to a heterologous gene.
  • One of ordinary skill in the art would recognize that the recombination results in a replacement of the endogenous promoter while retaining the gene in its native locus. Specific non-limiting examples are illustrated below in Table 8.
  • promoter cassettes can be readily incorporated into the genome of a host cell.
  • the promoter cassettes can be incorporated into host cells sequentially.
  • the recombinant vectors of the present disclosure provide for two or more different promoter cassettes in a single construct. The present specification provides no practical limit to the number of promoter replacements that can be developed using the described methods.
  • a plurality of host cells comprising a promoter ladder, wherein one cell of the plurality comprises a first promoter polynucleotide operably linked to a heterologous target gene, e.g. , an ancillary target gene, a shell 2 target gene, a shell 3 target gene, or a shell 4 target gene, and a second cell of the plurality comprises a second promoter polynucleotide operably linked to the same heterologous target gene, wherein the first and second promoter polynucleotides are different promoter polynucleotides of the promoter ladder.
  • a heterologous target gene e.g. , an ancillary target gene, a shell 2 target gene, a shell 3 target gene, or a shell 4 target gene
  • a second cell of the plurality comprises a second promoter polynucleotide operably linked to the same heterologous target gene, wherein the first and second promoter polynucleotides are different promoter polynucle
  • the plurality of host cells further comprise a third cell of the plurality comprising a third promoter polynucleotide operably linked to the same heterologous target gene, wherein the third promoter polynucleotide is a promoter polynucleotide of the promoter ladder that is different from the first and second promoter polynucleotides.
  • the plurality of host cells further comprise a fourth cell of the plurality comprising a fourth promoter polynucleotide operably linked to the same heterologous target gene, wherein the fourth promoter polynucleotide is a promoter polynucleotide of the promoter ladder that is different from the first, second, and third promoter polynucleotides.
  • the plurality of host cells further comprise a fifth cell of the plurality comprising a fifth promoter polynucleotide operably linked to the same heterologous target gene, wherein the fifth promoter polynucleotide is a promoter polynucleotide of the promoter ladder that is different from the first, second, third, and fourth promoter polynucleotides.
  • the plurality of host cells further comprise a sixth cell of the plurality comprising a sixth promoter polynucleotide operably linked to the same heterologous target gene, wherein the sixth promoter polynucleotide is a promoter polynucleotide of the promoter ladder that is different from the first, second, third, fourth, and fifth promoter polynucleotides.
  • the plurality of host cells further comprise a seventh cell of the plurality comprising a seventh promoter polynucleotide operably linked to the same heterologous target gene, wherein the seventh promoter polynucleotide is a promoter polynucleotide of the promoter ladder that is different from the first, second, third, fourth, fifth, and sixth promoter polynucleotides.
  • the plurality of host cells further comprise an eighth cell of the plurality comprising an eighth promoter polynucleotide operably linked to the same heterologous target gene, wherein the eighth promoter polynucleotide is a promoter polynucleotide of the promoter ladder that is different from the first, second, third, fourth, fifth, sixth, and seventh promoter polynucleotides.
  • each of the first, second, third, fourth, fifth, sixth, seventh, and/or eighth promoter polynucleotide of the promoter ladder is selected from SEQ ID NO: 1 -8.
  • the promoter polynucleotides of the promoter ladder are selected from SEQ ID NO: 1, 5, and 7.
  • the number of cells in the plurality can comprise at least about 1 x 10 5 , 1 x 10 6 , or 1 x 10 7 cells.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007-lysA and Pcg3121 -pgi. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcgl 860-pyc and Pcg0007-zwf. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007-lysA and Pcg0007-zwf. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3121-pck and Pcg0007-zwf.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007_39-ppc and Pcg0007-zwf. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3121-pck and Pcg3121 -pgi. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3381-ddh and Pcg0007-zwf. In an embodiment the host cell is a transgenic C.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007_265-dapB and Pcg0007- zwf In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007-zwf and Pcg3121-pgi. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3381 -ddh and Pcg3121 -pgi . In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3121 -pgi and Peg 1860- pyc. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcgl 860-pyc and Pcg0007_265-dapB. In an embodiment the host cell is a transgenic C.
  • glutamicum host cell comprising the promoter cassettes Pcgl 860-pyc and Pcg0007-lysA.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg l 860-asd and Pcg0007-zwf.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007_265-dapB and Pcg3121-pgi.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcgl860-pyc and Pcgl860-asd.
  • the host cell is a transgenic C.
  • glutamicum host cell comprising the promoter cassettes Pcg3381-aspB and Pcgl860-pyc.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3381-fbp and Pcgl860-pyc.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3381-ddh and Pcg3381-fbp.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0755-ptsG and Pcg3121-pgi.
  • the host cell is a transgenic C.
  • glutamicum host cell comprising the promoter cassettes Pcgl860-pyc and Pcg3121-pck.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcgl860-asd and Pcg3121-pgi.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcgl860-asd and Pcg3381-fbp.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007_39-lysE and Pcg3381-fbp.
  • the host cell is a transgenic C.
  • glutamicum host cell comprising the promoter cassettes Pcg3381-fbp and Pcg0007-lysA.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007_39-lysE and Pcgl860-pyc.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3121-pgi and Pcg3381-fbp.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3121-pck and Pcg0007-lysA.
  • the host cell is a transgenic C.
  • glutamicum host cell comprising the promoter cassettes Pcg0007-lysA and Pcg0007_265-dapB.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007_265-dapB and Pcgl860-asd.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3121-pgi and Pcg0007_265-dapD.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007-lysA and Pcg3381-ddh.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3121-pck and Pcgl 860-asd.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3121-pck and P
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3121-pck and Pcg0007_265-dapB. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3381-ddh and Pcgl860-asd. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007_39-ppc and Pcgl860-asd. In an embodiment the host cell is a transgenic C.
  • glutamicum host cell comprising the promoter cassettes Pcg0007_39-ppc and Pcg0007-lysA.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3381-ddh and
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007_265-dapB and Pcg3381-fbp. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007_39-ppc and Pcg0007_265-dapB. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3381-aspB and Pcg3121-pck. In an embodiment the host cell is a transgenic C.
  • glutamicum host cell comprising the promoter cassettes Pcg0007_265-dapB and Pcg0007_265-dapD.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007_39-lysE and Pcg3381-aspB.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007_39-lysE and Pcg0007_265-dapD.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3381-aspB and Pcg0007_265-dapB.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcgl 860-asd and Pcg0007_265-dapD. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3381-aspB and Pcg0007-lysA. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg3381-aspB and Pcg3381-ddh. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0755-ptsG and Pcgl 860-pyc.
  • the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0755-ptsG and Pcg3381-fbp. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0007-zwf and Pcg3381-fbp. In an embodiment the host cell is a transgenic C. glutamicum host cell comprising the promoter cassettes Pcg0755-ptsG and Pcg0007_265-dapD.
  • the present disclosure provides for, and includes, host cells having three or more promoter cassettes as described above.
  • the host cell includes the Pcg0007_39-zwf,
  • the host cell is a C.
  • the host cell includes any one of the foregoing promoter cassettes, and/or includes pcg0007_39-dnak; pcg0007_39-cg0074; pcg3121-cg0074; pcgl 860-rhle_609; pcg3121-cgl l44; pcg l 860-rhle_609; pcg0007_39-cg2899_2194; pcg0007_39-cgl486; pcg0007_39-cg2766; pcg0007_39- cmk; pcg0007_39-rpob_383; pcg0007_39-ddl; pcg0007_39-cg0027; pcg0007_39-ddl; pcg0007_39- rpob_383; pcg0007_39-rpob_383;
  • pcg0007_39-ncgl0767 pcg0007_39-ncgl l262, or a combination of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all thereof.
  • the promoter according to the invention or the expression unit according to the invention is furthermore used for improving the performance characteristics of microorganisms, which can include, for example, yield, titer, productivity, by-product elimination, tolerance to process excursions, optimal growth temperature and growth rate.
  • the promoter according to the invention or the expression unit according to the invention is used for up-regulating a target gene in a microorganism (overexpression).
  • Overexpression generally means an increase in the intracellular concentration or activity of a ribonucleic acid, a protein (polypeptide) or an enzyme in comparison with the starting strain (parent strain) or wild-type strain, if the latter is the starting strain.
  • the promoter according to the invention or the expression unit according to the invention is used for down-regulating a target gene in a microorganism (underexpression).
  • Underexpression generally means an decrease in the intracellular concentration or activity of a ribonucleic acid, a protein (polypeptide) or an enzyme in comparison with the starting strain (parent strain) or wild-type strain, if the latter is the starting strain.
  • a combination of promoters and/or expression units according to the invention are used for regulating expression of more than one target gene in a microorganism, wherein each target gene is either up-regulated or down-regulated.
  • the target genes up- or down-regulated by the combination of promoters and/or expression units are part of the same metabolic pathway.
  • the target genes up- or down-regulated by the combination of promoters and/or expression units are not part of the same metabolic pathway.
  • the promoters described herein can be used in combination with other methods very well-known in the art for attenuating (reducing or eliminating) the intracellular activity of one or more enzymes (proteins) in a microorganism which are coded by the corresponding DNA, for example by using a weak promoter or using a gene, or allele, which codes for a corresponding enzyme with a low activity, or inactivates the corresponding gene or enzyme (protein), and optionally combining these measures.
  • the reduction in gene expression can take place by suitable culturing or by genetic modification (mutation) of the signal structures of gene expression.
  • Signal structures of gene expression are, for example, repressor genes, activator genes, operators, promoters, attenuators, ribosome binding sites, the start codon and terminators.
  • the expert can find information on this e.g. in the patent application WO 96/15246, in Boyd and Murphy (Journal of Bacteriology 170: 5949 (1988)), in Voskuil and Chambliss (Nucleic Acids Research 26: 3548 ( 1998), in Jensen and Hammer (Biotechnology and Bioengineering 58: 191 ( 1998)), in Patek et al.
  • Possible mutations are transitions, transversions, insertions and deletions. Depending on the effect of the amino acid exchange on the enzyme activity, missense mutations or nonsense mutations are referred to. Insertions or deletions of at least one base pair in a gene lead to frame shift mutations, as a consequence of which incorrect amino acids are incorporated or translation is interrupted prematurely. Deletions of several codons typically lead to a complete loss of the enzyme activity. Instructions on generation of such mutations are prior art and can be found in known textbooks of genetics and molecular biology, such as e.g.
  • a central part of the coding region of the gene of interest is cloned in a plasmid vector which can replicate in a host (typically E. coli), but not in C. glutamicum.
  • Possible vectors are, for example, pSUP301 (Simon et al.
  • the plasmid vector which contains the central part of the coding region of the gene is then transferred into the desired strain of C. glutamicum by conjugation or transformation.
  • the method of conjugation is described, for example, by Schafer et al. (Applied and Environmental Microbiology 60, 756-759 (1994)). Methods for transformation are described, for example, by Thierbach et al.
  • a mutation such as e.g. a deletion, insertion or base exchange, is established in vitro in the gene of interest.
  • the allele prepared is in turn cloned in a vector which is not replicative for C. glutamicum and this is then transferred into the desired host of C.
  • the promoters described herein can be used in combination with other methods very well-known in the art for raising (enhancing) the intracellular activity of one or more enzymes in a microorganism that are coded by the corresponding DNA, by for example increasing the number of copies of the gene or genes, using a strong promoter, or using a gene that codes for a corresponding enzyme having a high activity, and optionally combining these measures.
  • the number of copies of the corresponding genes can be increased, or alternatively the promoter and regulation region or the ribosome binding site located upstream of the structure gene can be mutated.
  • Expression cassettes that are incorporated upstream of the structure gene act in the same way.
  • inducible promoters By means of inducible promoters it is in addition possible to increase the expression in the course of the enzymatic amino acid production.
  • the expression is similarly improved by measures aimed at prolonging the lifetime of the m-RNA.
  • the enzyme activity is also enhanced by preventing the degradation of the enzyme protein.
  • the genes or gene constructs may either be present in plasmids having different numbers of copies, or may be integrated and amplified in the chromosome. Alternatively, an overexpression of the relevant genes may furthermore be achieved by altering the composition of the media and the culture conditions.
  • Genes may be overexpressed for example by means of episomal plasmids.
  • Suitable plasmids are those that are replicated in coryneform bacteria.
  • Numerous known plasmid vectors such as for example pZl (Menkel et al , Applied and Environmental Microbiology ( 1989) 64: 549-554), pEKExl (Eikmanns et al. , Gene 102:93-98 ( 1991)) or pHS2-l (Sonnen et al. , Gene 107:69-74 (1991)) are based on the cryptic plasmids pHM1519, pBLl or pGAl .
  • plasmid vectors such as for example those based on pCG4 (U.S. Pat. No. 4,489, 160), or pNG2 (Serwold-Davis et al , FEMS Microbiology Letters 66, 1 19-124 (1990)), or pAGl (U.S. Pat. No. 5, 158,891) may be used in a similar way.
  • plasmid vectors with the aid of which the process of gene amplification by integration in the chromosome can be employed, such as has been described for example by Reinscheid et al. (Applied and Environmental Microbiology 60, 126-132 (1994)) for the duplication and amplification of the hom-thrB operon.
  • the complete gene is cloned into a plasmid vector that can replicate in a host (typically E. coli) but not in C. glutamicum.
  • Suitable vectors are for example pSUP301 (Simon et al.
  • the plasmid vector that contains the gene to be amplified is then transferred by conjugation or transformation into the desired strain of C. glutamicum .
  • the method of conjugation is described for example in Schafer et al. (Applied and Environmental Microbiology 60, 756-759 (1994)). Transformation methods are described for example in Thierbach et al.
  • Methods of regulating, / ' . e. , either increasing or decreasing, gene expression include recombinant methods in which a microorganism is produced using a DNA molecule provided in vitro.
  • DNA molecules comprise, for example, promoters, expression cassettes, genes, alleles, coding regions, etc. They are introduced into the desired microorganisms by methods of transformation, conjugation, transduction or similar methods .
  • the promoters are preferably a polynucleotide of SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO: 6, SEQ ID NO:7, or SEQ ID NO: 8, and the expression cassettes are preferably a polynucleotide of SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO: 7, or SEQ ID NO: 8 which, via the nucleotide at its 3 ' end, are functionally linked to a linker polynucleotide which ensures translation of RNA.
  • the measures of overexpression using the promoter according to the invention or the expression unit according to the invention increase the activity or concentration of the corresponding polypeptide usually by at least 10%, 25%, 50%, 75%, 100%, 150%, 200%, 300%, 400% or 500%, preferably by no more than 1,000%, 2,000%, 4,000%, 10,000% or 20,000%, based on the activity or concentration of said polypeptide in the strain prior to the measure resulting in overexpression.
  • the extent of expression or overexpression may be established by measuring the amount of mRNA transcribed from the gene, by determining the amount of polypeptide and by determining enzyme activity.
  • the amount of mRNA may be determined inter alia by using the methods of "Northern Blotting" and of quantitative RT-PCR. Quantitative RT-PCR involves reverse transcription which precedes the polymerase chain reaction. For this, the LightCyclerTM System from Roche Diagnostics (Boehringer Mannheim GmbH, Roche Molecular Biochemicals, Mannheim, Germany) may be used, as described in Jungwirth et al. (FEMS Microbiology Letters 281, 190-197 (2008)), for example. The concentration of the protein may be determined via 1- and 2-dimensional protein gel fractionation and subsequent optical identification of the protein concentration using appropriate evaluation software in the gel. A customary method of preparing protein gels for coryneform bacteria and of identifying said proteins is the procedure described by Hermann et al.
  • the protein concentration may likewise be determined by Western-Blot hybridization using an antibody specific for the protein to be detected (Sambrook et al , Molecular cloning: a laboratory manual. 2nd Ed. Cold Spring Harbor
  • the measure of overexpressing target genes using the promoter according to the invention may be combined in a suitable manner with further overexpression measures.
  • Overexpression is achieved by a multiplicity of methods available in the prior art. These include increasing the copy number in addition to modifying the nucleotide sequences which direct or control expression of the gene.
  • the copy number may be increased by means of plasmids which replicate in the cytoplasm of the microorganism. To this end, an abundance of plasmids are described in the prior art for very different groups of microorganisms, which plasmids can be used for setting the desired increase in the copy number of the gene. Plasmids suitable for the genus Corynebacterium are described, for example, in Tauch et al. (Journal of Biotechnology 104 ( 1- 3), 27-40, (2003)), and in Stansen et al. (Applied and Environmental Microbiology 71, 5920-5928 (2005)).
  • the copy number may furthermore be increased by at least one (1) copy by introducing further copies into the chromosome of the microorganism.
  • Methods suitable for the genus Corynebacterium are described, for example, in the patents WO 03/014330, WO 03/040373 and WO 04/069996.
  • Gene expression may furthermore be increased by positioning a plurality of promoters upstream of the target gene or functionally linking them to the gene to be expressed and achieving increased expression in this way. Examples of this are described in the patent WO 2006/06971 1.
  • Transcription of a gene is controlled, where appropriate, by proteins which suppress (repressor proteins) or promote (activator proteins) transcription. Accordingly, overexpression can likewise be achieved by increasing the expression of activator proteins or reducing or switching off the expression of repressor proteins or else eliminating the binding sites of the repressor proteins.
  • the rate of elongation is influenced by the codon usage, it being possible to enhance translation by utilizing codons for transfer R As (tR As) which are frequent in the starting strain. Moreover, replacing a start codon with the ATG codon most frequent in many microorganisms (77% in E.
  • coli may considerably improve translation, since, at the R A level, the AUG codon is two to three times more effective than the codons GUG and UUG, for example (Khudyakov et al , FEBS Letters 232(2):369-71( 1988); Reddy et al , Proceedings of the National Academy of Sciences of the USA 82(17):5656-60 (1985)). It is also possible to optimize the sequences surrounding the start codon because synergistic effects between the start codon and the flanking regions have been described (Stenstrom et al , Gene 273(2):259-65 (2001); Hui et al , EMBO Journal 3(3):623-9 ( 1984)).
  • the disclosure also relates to vectors comprising the polynucleotides according to the invention.
  • Kirchner and Tauch describe a selection of vectors to be used in C. glutamicum.
  • Homologous recombination using the vectors according to the invention allows DNA segments on the chromosome to be replaced with polynucleotides according to the invention which are transported into the cell by the vector.
  • the DNA region to be replaced with the polynucleotide according to the invention is provided at the ends with nucleotide sequences homologous to the target site which determine the site of integration of the vector and of replacement of the DNA.
  • promoter polynucleotide according to the invention may: 1) be replaced with the native promoter at the native gene locus of the target gene in the chromosome; or 2) be integrated with the target gene at the native gene locus of the latter or at another gene locus.
  • Replacement of the native promoter at the native gene locus of the target gene means the fact that the naturally occurring promoter of the gene which usually is naturally present by way of a single copy at its gene locus in the corresponding wild type or corresponding starting organism in the form of its nucleotide sequence is replaced.
  • “Another gene locus” means a gene locus whose nucleotide sequence is different from the sequence of the target gene. Said other gene locus or the nucleotide sequence at said other gene locus is preferably located within the chromosome and normally is not essential for growth and for production of the desired chemical compounds. It is furthermore possible to use intergenic regions within the chromosome, i. e. nucleotide sequences without coding function.
  • Expression or overexpression is preferably carried out in microorganisms of the genus
  • Corynebacterium Within the genus Corynebacterium, preference is given to strains based on the following species: C. efficiens, with the deposited type strain being DSM44549, C. glutamicum, with the deposited type strain being ATCC 13032, and C. ammoniagenes, with the deposited type strain being ATCC6871. Very particular preference is given to the species C. glutamicum.
  • Suitable strains of the genus Corynebacterium, in particular of the species Corynebacterium glutamicum, are in particular the known wild-type strains: Corynebacterium glutamicum ATCC13032, Corynebacterium acetoglutamicum ATCC15806, Corynebacterium acetoacidophilum ATCC13870, Corynebacterium melassecola ATCC 17965, Corynebacterium thermoaminogenes FERM BP-1539, Brevibacterium flavum ATCC14067, Brevibacterium lactofermentum ATCC13869, and Brevibacterium divaricatum ATCC14020; and L-amino acid-producing mutants, or strains, prepared therefrom, such as, for example, the L-lysine-producing strains: Corynebacterium glutamicum FERM-P 1709,
  • C. efficiens have also been referred to as C. thermoaminogenes in the prior art, such as the strain FERM BP-1539, for example.
  • microorganisms or strains (starting strains) employed for the expression or overexpression measures according to the invention preferably already possess the ability to secrete a desired fine chemical into the surrounding nutrient medium and accumulate there.
  • the expression "to produce” is also used for this herein below.
  • the strains employed for the overexpression measures possess the ability to accumulate the desired fine chemical in concentrations of at least 0.10 g/L, at least 0.25 g/L, at least 0.5 g/L, at least 1.0 g/L, at least 1.5 g/L, at least 2.0 g/L, at least 4.0 g/L, or at least 10.0 g/L in no more than 120 hours, no more than 96 hours, no more than 48 hours, no more than 36 hours, no more than 24 hours, or no more than 12 hours in the cell or in the nutrient medium.
  • the starting strains are preferably strains prepared by mutagenesis and selection, by recombinant DNA technologies or by a combination of both methods.
  • a microorganism suitable for the measures of the invention may also be obtained by firstly employing the promoter according to the invention, e.g. , SEQ ID NO: l, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO: 8 for overexpression or underexpression of the target genes in a wild strain such as, for example, the C. glutamicum type strain ATCC 13032 or the strain ATCC 14067, and then, by means of further genetic measures described in the prior art, causing the microorganism to produce the desired fine chemical(s).
  • a wild strain such as, for example, the C. glutamicum type strain ATCC 13032 or the strain ATCC 14067
  • biomolecules means with regard to the measures of the invention amino acids, organic acids, vitamins, nucleosides and nucleotides. Particular preference is given to proteinogenic amino acids, non-proteinogenic amino acids, macromolecules, and organic acids.
  • Proteinogenic amino acids mean the amino acids which occur in natural proteins, / ' . e. in proteins of microorganisms, plants, animals and humans. They serve as structural units for proteins in which they are linked to one another via peptide bonds.
  • L-amino acids or amino acids are mentioned hereinbelow, they are to be understood as meaning one or more amino acids, including their salts, selected from the group L-asparagine, L- threonine, L-serine, L-glutamate, L-glycine, L-alanine, L-cysteine, L-valine, L-methionine, L-isoleucine, L-leucine, L-tyrosine, L-phenylalanine, L-histidine, L-lysine, L-tryptophan and L-arginine.
  • L-lysine is especially preferred.
  • L-Amino acids in particular lysine
  • lysine are used in human medicine and in the pharmaceuticals industry, in the foodstuffs industry and very particularly in animal nutrition. There is therefore a general interest in providing new improved processes for the preparation of amino acids, in particular L-lysine.
  • protein and polypeptide are interchangeable.
  • the present disclosure provides a microorganism which produces a fine chemical, said microorganism having increased expression of one or more genes in comparison to the particular starting strain by using a promoter of a promoter ladder, such as a promoter selected from SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO:8.
  • a promoter of a promoter ladder such as a promoter selected from SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO:8.
  • the present disclosure furthermore provides a process for fermentative preparation of a fine chemical, comprising the steps of:
  • microorganisms produced may be cultured continuously— as described, for example, in WO 05/021772— or discontinuously in a batch process (batch cultivation) or in a fed-batch or repeated fed-batch process for the purpose of producing the desired organic -chemical compound.
  • the culture medium or fermentation medium to be used must in a suitable manner satisfy the demands of the respective strains. Descriptions of culture media for various microorganisms are present in the "Manual of Methods for General Bacteriology" of the American Society for Bacteriology
  • culture medium and fermentation medium are
  • sugars and carbohydrates such as, for example, glucose, sucrose, lactose, fructose, maltose, molasses, sucrose-containing solutions from sugar beet or sugar cane processing, starch, starch hydrolysate, and cellulose; oils and fats such as, for example, soybean oil, sunflower oil, groundnut oil and coconut fat; fatty acids such as, for example, palmitic acid, stearic acid, and linoleic acid; alcohols such as, for example, glycerol, methanol, and ethanol; and organic acids such as, for example, acetic acid or lactic acid.
  • sugars and carbohydrates such as, for example, glucose, sucrose, lactose, fructose, maltose, molasses, sucrose-containing solutions from sugar beet or sugar cane processing, starch, starch hydrolysate, and cellulose; oils and fats such as, for example, soybean oil, sunflower oil, groundnut oil and coconut fat; fatty acids such as, for
  • nitrogen source organic nitrogen-containing compounds such as peptones, yeast extract, meat extract, malt extract, corn steep liquor, soybean flour, and urea; or inorganic compounds such as ammonium sulfate, ammonium chloride, ammonium phosphate, ammonium carbonate, and ammonium nitrate.
  • organic nitrogen-containing compounds such as peptones, yeast extract, meat extract, malt extract, corn steep liquor, soybean flour, and urea
  • inorganic compounds such as ammonium sulfate, ammonium chloride, ammonium phosphate, ammonium carbonate, and ammonium nitrate.
  • the nitrogen sources can be used individually or as a mixture.
  • the culture medium may additionally comprise salts, for example in the form of chlorides or sulfates of metals such as, for example, sodium, potassium, magnesium, calcium and iron, such as, for example, magnesium sulfate or iron sulfate, which are necessary for growth.
  • salts for example in the form of chlorides or sulfates of metals such as, for example, sodium, potassium, magnesium, calcium and iron, such as, for example, magnesium sulfate or iron sulfate, which are necessary for growth.
  • essential growth factors such as amino acids, for example homoserine and vitamins, for example thiamine, biotin or pantothenic acid, may be employed in addition to the abovementioned substances.
  • Said starting materials may be added to the culture in the form of a single batch or be fed in during the cultivation in a suitable manner.
  • the pH of the culture can be controlled by employing basic compounds such as sodium hydroxide, potassium hydroxide, ammonia, or aqueous ammonia; or acidic compounds such as phosphoric acid or sulfuric acid in a suitable manner.
  • the pH is generally adjusted to a value of from 6.0 to 8.5, preferably 6.5 to 8.
  • antifoams such as, for example, fatty acid polyglycol esters.
  • suitable selective substances such as, for example, antibiotics.
  • the fermentation is preferably carried out under aerobic conditions. In order to maintain these conditions, oxygen or oxygen-containing gas mixtures such as, for example, air are introduced into the culture.
  • liquids enriched with hydrogen peroxide are used.
  • the fermentation is carried out, where appropriate, at elevated pressure, for example at an elevated pressure of from 0.03 to 0.2 MPa.
  • the temperature of the culture is normally from 20 °C to 45 °C and preferably from 25 °C to 40 °C, particularly preferably from 30 °C to 37 °C.
  • the cultivation is preferably continued until an amount of the desired organic-chemical compound sufficient for being recovered has formed. This aim is normally achieved within 10 hours to 160 hours. In continuous processes, longer cultivation times are possible.
  • the activity of the microorganisms results in a concentration (accumulation) of the organic-chemical compound in the fermentation medium and/or in the cells of said microorganisms.
  • Analysis of L-amino acids to determine the concentration at one or more time(s) during the fermentation can take place by separating the L-amino acids by means of ion exchange chromatography, preferably cation exchange chromatography, with subsequent post-column derivatization using ninhydrin, as described in Spackman et al. (Analytical Chemistry 30: 1190-1206 ( 1958)). It is also possible to employ or ⁇ 20-phthaldialdehyde rather than ninhydrin for post-column derivatization. An overview article on ion exchange chromatography can be found in Pickering (LC-GC Magazine of Chromatographic Science) 7(6), 484-487 ( 1989)).
  • Detection is carried out photometrically (absorption, fluorescence).
  • Determination of the concentration of a-ketoacids at one or more time point(s) in the course of the fermentation may be carried out by separating the ketoacids and other secreted products by means of ion exchange chromatography, preferably cation exchange chromatography, on a sulfonated styrene- divinylbenzene polymer in the H+ form, for example by means of 0.025 M sulfuric acid with subsequent UV detection at 215 nm (alternatively also at 230 or 275 nm).
  • a REZEK RFQ - Fast Fruit H+ column may be employed, but other suppliers for the separating phase (e.g. Aminex from BioRad) are feasible. Similar separations are described in application examples by the suppliers.
  • the performance of the processes or fermentation processes containing the promoter variants according to the invention in terms of one or more of the parameters selected from the group of concentration (compound formed per unit volume), yield (compound formed per unit carbon source consumed), formation (compound formed per unit volume and time) and specific formation (compound formed per unit dry cell matter or dry biomass and time or compound formed per unit cellular protein and time) or else other process parameters and combinations thereof, is increased by at least 0.5%, at least 1%, at least 1.5%, at least 2%, at least 3%, at least 4%, at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 100% based on processes or fermentation processes using microorganisms not containing the promoter variants according to the invention. This is considered to be very worthwhile in terms of a large-scale industrial process.
  • the fermentation measures result in a fermentation broth which contains the desired fine chemical, preferably amino acids, organic acids, vitamins, nucleosides or nucleotides.
  • a product containing the fine chemical is then provided or produced or recovered in liquid or solid form.
  • a fermentation broth means a fermentation medium or nutrient medium in which a
  • microorganism has been cultivated for a certain time and at a certain temperature.
  • the fermentation medium or the media employed during fermentation comprise(s) all the substances or components which ensure production of the desired compound and typically propagation and viability.
  • the resulting fermentation broth accordingly comprises: a) the biomass (cell mass) of the microorganism, said biomass having been produced due to propagation of the cells of said microorganism;
  • the constituents of the fermentation medium employed or of the starting materials such as, for example, vitamins such as biotin or salts such as magnesium sulfate, which have not been consumed in the fermentation.
  • the organic byproducts include substances which are produced by the microorganisms employed in the fermentation in addition to the particular desired compound and are optionally secreted.
  • the fermentation broth is removed from the culture vessel or fermentation tank, collected where appropriate, and used for providing a product containing the fine chemical in liquid or solid form.
  • the expression "recovering the fine chemical-containing product” is also used for this.
  • the fine chemical-containing fermentation broth itself which has been removed from the fermentation tank, constitutes the recovered product.
  • One or more of the measures selected from the group consisting of
  • the partial (> 0% to ⁇ 80%) to complete ( 100%) or virtually complete (> 80% to ⁇ 100%) removal of the water (measure a)) is also referred to as drying.
  • the biomass can be removed wholly or partly from the fermentation broth by separation methods such as, for example, centrifugation, filtration, decantation or a combination thereof, or be left completely therein.
  • separation methods such as, for example, centrifugation, filtration, decantation or a combination thereof, or be left completely therein.
  • the biomass or the biomass-containing fermentation broth is inactivated during a suitable process step, for example by thermal treatment (heating) or by addition of acid.
  • the biomass is completely or virtually completely removed so that no (0%) or at most 30%, at most 20%, at most 10%, at most 5%, at most 1% or at most 0.1% biomass remains in the prepared product.
  • the biomass is not removed, or is removed only in small proportions, so that all ( 100%) or more than 70%, 80%, 90%, 95%, 99% or 99.9% biomass remains in the product prepared.
  • the biomass is removed in proportions of from > 0% to ⁇ 100%.
  • the fermentation broth obtained after the fermentation can be adjusted, before or after the complete or partial removal of the biomass, to an acidic pH with an inorganic acid such as, for example, hydrochloric acid, sulfuric acid, or phosphoric acid; or organic acid such as, for example, propionic acid, so as to improve the handling properties of the final product (GB 1,439,728 or EP 1 331220). It is likewise possible to acidify the fermentation broth with the complete content of biomass.
  • the broth can also be stabilized by adding sodium bisulfite (NaHC0 3 , GB 1,439,728) or another salt, for example ammonium, alkali metal, or alkaline earth metal salt of sulfurous acid.
  • any organic or inorganic solids present in the fermentation broth are partially or completely removed.
  • the organic byproducts dissolved in the fermentation broth, and the dissolved unconsumed constituents of the fermentation medium (starting materials) remain at least partly (> 0%), preferably to an extent of at least 25%, particularly preferably to an extent of at least 50% and very particularly preferably to an extent of at least 75% in the product. Where appropriate, they also remain completely (100%) or virtually completely, meaning > 95% or > 98% or > 99%, in the product. If a product in this sense comprises at least part of the constituents of the fermentation broth, this is also described by the term "product based on fermentation broth”.
  • water is removed from the broth, or said broth is thickened or concentrated, by known methods such as, for example, using a rotary evaporator, thin-film evaporator, falling-film evaporator, by reverse osmosis or by nanofiltration.
  • This concentrated fermentation broth can then be worked up to free-flowing products, in particular to a fine powder or preferably coarse granules, by methods of freeze drying, spray drying, spray granulation or by other processes such as in the circulating fluidized bed, as described for example according to PCT/EP2004/006655.
  • a desired product is isolated where appropriate from the resulting granules by screening or dust removal. It is likewise possible to dry the fermentation broth directly, i.e. without previous concentration by spray drying or spray granulation.
  • Free-flowing means powders which, from a series of glass orifice vessels with orifices of different sizes, flow unimpeded at least out of the vessel with a 5 mm orifice (Klein: Seifen, Ole, Fette, Wachse 94, 12 (1968)).
  • “Fine” means a powder predominantly (> 50%) having a particle size of diameter from 20 to 200 um.
  • Coarse means a product predominantly (> 50%) of a particle size of diameter from 200 to 2000 um.
  • the particle size determination can be carried out by methods of laser diffraction spectrometry. Corresponding methods are described in the textbook “TeilchengroBenshot in der Laborpraxis” by R. H. Miiller and R. Schuhmann,ticianliche Verlagsgesellschaft Stuttgart (1996) or in the text book “Introduction to Particle Technology” by M. Rhodes, published by Wiley &Sons (1998).
  • the free-flowing, fine powder can in turn be converted by suitable compaction or granulation processes into a coarse, very free-flowing, storable and substantially dust-free product.
  • dust-free means that the product comprises only small proportions ( ⁇ 5%) of particle sizes below 100 um in diameter.
  • Storable in the sense of this invention means a product which can be stored for at least one (1) year or longer, preferably at least 1.5 years or longer, particularly preferably two (2) years or longer, in a dry and cool environment without any substantial loss of the respective organic -chemical compound occurring.
  • Substantial loss means a loss of >5%.
  • organic or inorganic auxiliaries or carriers such as starch, gelatin, cellulose derivatives or similar substances, as normally used in the processing of food products or feeds as binders, gelling agents or thickeners, or further substances such as, for example, silicas, silicates (EP0743016A) and stearates.
  • oils or fats are mineral oils, vegetable oils or mixtures of vegetable oils. Examples of such oils are soybean oil, olive oil, soybean oil/lecithin mixtures. In the same way, silicone oils, polyethylene glycols or hydroxyethylcellulose are also suitable.
  • Treatment of the surfaces of the granules with said oils achieves an increased abrasion resistance of the product and a reduction in the dust content.
  • the oil content in the product is 0.02 to 2.0% by weight, preferably 0.02 to 1.0% by weight, and very particularly preferably 0.2 to 1.0% by weight, based on the total amount of the feed additive.
  • Preferred products have a proportion of > 97% by weight with a particle size of from 100 to 1800 um or a proportion of > 95% by weight with a particle size of diameter 300 to 1800 um.
  • the proportion of dust, i.e. particles with a particle size ⁇ 100 pm, is preferably > 0 to 1% by weight, particularly preferably not exceeding 0.5% by weight.
  • the product may also be absorbed on an organic or inorganic carrier known and customary in the processing of feeds, such as, for example, silicas, silicates, meals, brans, flours, starches, sugars or others, and/or be mixed and stabilized with customary thickeners or binders. Examples of use and processes therefor are described in the literature (Die Miihle + Mischfuttertechnik 132 ( 1995) 49, page 817).
  • the promoters of the present disclosure are useful for improved processes for the production of biomolecules in host cells.
  • An example of the application and use of the promotor of the present disclosure is directed to the production of the amino acid L-lysine.
  • Fig. l presents the biosynthetic pathway for the production of L-lysine and includes the genes pck, odx, icd, and horn (e.g. , the homoserine/threonine synthase pathway), that divert intermediates from the pathway leading to reductions in overall L-lysine yield.
  • the symbols, gene names, Enzyme Commission number (EC number), and map position in C. glutamicum strain ATCC 13032 are provided in Table 3.
  • Recombinant vectors comprising a promoter of SEQ ID NOs: 1 to 8 functionally linked to a target gene as provided in Table 3 are cloned into Corynebacterium cloning vectors using yeast homologous recombination cloning techniques to assemble a vector in which each promoter was flanked by direct repeat regions to provide for homologous recombination in Corynebacterium glutamicum at the target gene locus.
  • the endogenous promoter is replaced by the promoter of SEQ ID NOs: 1 to 8 functionally linked to the respective target gene in the endogenous C. glutamicum locus.
  • a variety of targeting vectors comprising the promoter and functionally linked target gene included a range of homology direct repeat arm lengths ranging from 0.5Kb, 1Kb, 2Kb, and 5Kb.
  • Each DNA insert was produced by PCR amplification of homologous regions using commercially sourced oligos and the host strain genomic DNA described above as template.
  • the promoter to be introduced into the genome was encoded in the oligo tails.
  • PCR fragments were assembled into the vector backbone using homologous recombination in yeast.
  • Vectors are initially transformed into E.coli using standard heat shock transformation techniques and correctly assembled clones are identified and validated. Transformed E.coli bacteria are tested for assembly success. Four colonies from each E. coli transformation plate are cultured and tested for correct assembly via PCR. Vectors are amplified in the E. coli hosts to provide vector DNA for Corynebacterium transformation.
  • Validated clones are transformed into Corynebacterium glutamicum host cells via
  • CFUs Colony Forming Units
  • Sucrose resistance frequency for various homology direct repeat arms do not vary significantly with arm length. These results suggest that loopout efficiencies remain steady across homology arm lengths of 0.5 kb to 5kb.
  • Sequencing results show a 10-20% efficiency in loop outs. Not to be limited by any particular theory, loop-out may be dependent on insert sequence. Even if correct, picking 10-20 sucrose-resistant colonies leads to high success rates.
  • the recombinant vectors replace the endogenous promoter sequences with a promoter selected from the group consisting of Pcgl860 (SEQ ID NO:2), Pcg0007 (SEQ ID NO:3), Pcg0755 (SEQ ID NO:4), Pcg0007_lib_265 (SEQ ID NO:5), Pcg3381 (SEQ ID NO:6), Pcg007_lib_l 19 (SEQ ID NO: 7), and Pcg3121 (SEQ ID NO: 8).
  • the resulting recombinant strains is provided in the following list:
  • Pcg0007_119-dapA Pcg0007_265-dapB; Pcg0755-dapB; Pcg0007-dapB; Pcg3381-dapB; Pcgl860-dapB Pcg3121-dapB; Pcg0007_119-dapB; Pcg0007_265-dapD; Pcg0007_119-dapD; Pcg3381-dapD;
  • Pcg0007_39-dapD Pcg3121-dapD; Pcg0007-dapD; Pcgl860-dapD; Pcg0755-dapD; Pcg3381-dapE; Pcg3121-dapE; Pcg0755-dapE; Pcg0007_119-dapE; Pcgl860-dapE; Pcg0007_39-dapE; Pcg0007_265- dapF; Pcg3381-dapF; Pcg0007_119-dapF; Pcg0007-dapF; Pcgl860-dapF; Pcg0007_39-dapF; Pcg3381- ddh; Pcg3121-ddh; Pcg0007_119-ddh; Pcg0007_39-ddh; Pcgl860-ddh; P
  • the yield of L-lysine is increased by over 24% (e.g. , recombinant strain
  • the yield of L-lysine is decreased by nearly 90% (e.g., recombinant strain 700000773).
  • Replacement of the promoter for the pgi and zwf results in greater than 10% improvements to L-lysine production.
  • L-lysine yield is maximized by a relatively weak promoter (e.g. , pgi having relative promoter expression of 1, 7x, or 48x, or dapB at a relative promoter strength of 7x) or maximized by intermediate expression (e.g., lysA at having a relative promoter expression of 454x).
  • expression is maximal when the relative promoter strength is maximized (e.g. , ppc).
  • the location of the gene in the genetic pathway does not reliably predict the relative increase or decrease in L-lysine yield or the optimal promoter strength. For example, high level expression of cg0931 results in improved yield while higher levels of dapD result in no improvement or decreased yield.
  • Example 1 The yield of L-lysine is modified by swapping pairs of promoters for target genes.
  • the constructs of Example 1 are used to prepare recombinant organsims as follows:
  • Example 3 Engineering the L-lysine biosynthetic pathway with promoters operably linked to off- pathway genes
  • the yield of L-lysine is modified by including a second promoter polynucleotide sequence functionally linked to an off-pathway second heterologous target gene.
  • the heterologous target genes are selected from ncgl0009, ncgl0019, ncgl0054, ncgl0082, ncgl0142, ncgl0223, ncgl0241, ncgl0242, ncgl0304, ncgl0306, ncgl0356, ncgl0398, ncgl0408, ncgl0424, ncgl0425, ncgl0427, ncgl0439, ncgl0458, nq $10471, nq 5IO53 I, nq 510546, nq 510564, nq 5IO573, nq 510578, nq 510581, nq 510598, n
  • Constructs containing a promoter identified herein linked to sequences homologous to a portion of the heterologous off-pathway genes identified above are used to prepare recombinant host cell organisms as provided in Tables 8 and 9.
  • the recombinant vectors replace the endogenous promoter sequences with a promoter selected from the group consisting of Peg 1860 (SEQ ID NO:2), Pcg0007 (SEQ ID NO:3), Pcg0755 (SEQ ID NO:4), Pcg0007_lib_265 (SEQ ID NO: 5), Pcg3381 (SEQ ID NO:6), Pcg007_lib_l 19 (SEQ ID NO:7), and Pcg3121 (SEQ ID NO: 8).
  • a list of the resulting recombinant strains is provided below in Table 8.
  • the yield of L-lysine is increased by over 14% (e.g. , recombinant strain 7000152451) over the parent strain that does not contain a heterologous promoter functionally linked to an off-pathway target gene.
  • the best performing modifications overall are pcg0007_39-cg0725 (average of 6.5% yield change in six strains), pcg0007_39-ncgll262 (average of 6.3% yield change in nine strains), and pcg0007_39-cg2766 (average of 5.1% yield change in 23 strains).
  • L-lysine is not a simple dependence on incorporating the most active promoters.
  • the pcg3121-mutm2_2522 modification involves a weak promoter but improved yield by an average of 5% in four strains.
  • Table 8 Recombinant strains of C. glutamicum having modified expression of non-L-lysine Biosynthetic Genes and yield change from base of at least 3%, where the promoter-target modification has been applied in at least five different strain backgrounds
  • nusg 2 pcg3121- 3 GO:0004518;GO:0016829;GO:0006950;GO:0016798;GO:0034641;GO
  • rpob_383 9 0016779 pcg0007_39- 4 GO:0034641;GO:0003674;GO:0001071;GO:0003677;GO:0008150;GO
  • ncgl0306 7 0004871;GO:0003674;GO:0007165
  • ncgll961 0034641;GO:0008150;GO:0044281;GO:0006790 pcg0007_39- GO:0034641;GO:0008150;GO:0044281;GO:0003674;GO:0016874;GO
  • ncgll880 0003677;GO:0006259;GO:0008150
PCT/US2018/036472 2017-06-07 2018-06-07 Promoters from corynebacterium glutamicum and uses thereof in regulating ancillary gene expression WO2018226964A2 (en)

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